Starting phenix.real_space_refine on Sat Mar 2 06:49:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyn_8618/03_2024/5uyn_8618_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyn_8618/03_2024/5uyn_8618.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyn_8618/03_2024/5uyn_8618_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyn_8618/03_2024/5uyn_8618_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyn_8618/03_2024/5uyn_8618_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyn_8618/03_2024/5uyn_8618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyn_8618/03_2024/5uyn_8618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyn_8618/03_2024/5uyn_8618_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyn_8618/03_2024/5uyn_8618_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.325 sd= 1.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4806 5.49 5 S 172 5.16 5 C 77683 2.51 5 N 28568 2.21 5 O 42488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "05 ARG 13": "NH1" <-> "NH2" Residue "05 ARG 33": "NH1" <-> "NH2" Residue "05 ARG 59": "NH1" <-> "NH2" Residue "05 ARG 77": "NH1" <-> "NH2" Residue "05 ARG 83": "NH1" <-> "NH2" Residue "05 ARG 169": "NH1" <-> "NH2" Residue "05 ARG 184": "NH1" <-> "NH2" Residue "06 ARG 21": "NH1" <-> "NH2" Residue "06 ARG 44": "NH1" <-> "NH2" Residue "06 ARG 49": "NH1" <-> "NH2" Residue "06 ARG 61": "NH1" <-> "NH2" Residue "06 ARG 88": "NH1" <-> "NH2" Residue "06 ARG 102": "NH1" <-> "NH2" Residue "06 ARG 162": "NH1" <-> "NH2" Residue "06 ARG 170": "NH1" <-> "NH2" Residue "07 ARG 70": "NH1" <-> "NH2" Residue "07 ARG 79": "NH1" <-> "NH2" Residue "07 ARG 91": "NH1" <-> "NH2" Residue "07 ARG 101": "NH1" <-> "NH2" Residue "07 ARG 109": "NH1" <-> "NH2" Residue "07 ARG 111": "NH1" <-> "NH2" Residue "07 ARG 114": "NH1" <-> "NH2" Residue "07 ARG 132": "NH1" <-> "NH2" Residue "08 ARG 2": "NH1" <-> "NH2" Residue "08 PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "08 ARG 152": "NH1" <-> "NH2" Residue "08 ARG 162": "NH1" <-> "NH2" Residue "08 ARG 169": "NH1" <-> "NH2" Residue "12 ARG 13": "NH1" <-> "NH2" Residue "12 ARG 37": "NH1" <-> "NH2" Residue "12 ARG 96": "NH1" <-> "NH2" Residue "12 ARG 120": "NH1" <-> "NH2" Residue "14 ARG 21": "NH1" <-> "NH2" Residue "14 ARG 33": "NH1" <-> "NH2" Residue "14 ARG 41": "NH1" <-> "NH2" Residue "14 ARG 47": "NH1" <-> "NH2" Residue "14 ARG 60": "NH1" <-> "NH2" Residue "14 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 ARG 78": "NH1" <-> "NH2" Residue "14 ARG 126": "NH1" <-> "NH2" Residue "15 ARG 10": "NH1" <-> "NH2" Residue "15 ARG 18": "NH1" <-> "NH2" Residue "15 ARG 40": "NH1" <-> "NH2" Residue "15 ARG 44": "NH1" <-> "NH2" Residue "15 ARG 50": "NH1" <-> "NH2" Residue "15 ARG 55": "NH1" <-> "NH2" Residue "15 ARG 59": "NH1" <-> "NH2" Residue "15 ARG 114": "NH1" <-> "NH2" Residue "16 ARG 8": "NH1" <-> "NH2" Residue "16 ARG 12": "NH1" <-> "NH2" Residue "16 ARG 17": "NH1" <-> "NH2" Residue "16 ARG 22": "NH1" <-> "NH2" Residue "16 ARG 46": "NH1" <-> "NH2" Residue "16 ARG 63": "NH1" <-> "NH2" Residue "16 ARG 64": "NH1" <-> "NH2" Residue "16 ARG 69": "NH1" <-> "NH2" Residue "16 ARG 71": "NH1" <-> "NH2" Residue "16 ARG 96": "NH1" <-> "NH2" Residue "16 ARG 118": "NH1" <-> "NH2" Residue "17 ARG 10": "NH1" <-> "NH2" Residue "17 ARG 16": "NH1" <-> "NH2" Residue "17 ARG 25": "NH1" <-> "NH2" Residue "17 ARG 81": "NH1" <-> "NH2" Residue "17 ARG 94": "NH1" <-> "NH2" Residue "17 ARG 102": "NH1" <-> "NH2" Residue "17 ARG 111": "NH1" <-> "NH2" Residue "18 ARG 20": "NH1" <-> "NH2" Residue "18 ARG 38": "NH1" <-> "NH2" Residue "18 ARG 61": "NH1" <-> "NH2" Residue "18 ARG 88": "NH1" <-> "NH2" Residue "18 ARG 100": "NH1" <-> "NH2" Residue "18 ARG 108": "NH1" <-> "NH2" Residue "19 ARG 2": "NH1" <-> "NH2" Residue "19 ARG 5": "NH1" <-> "NH2" Residue "19 ARG 12": "NH1" <-> "NH2" Residue "19 ARG 32": "NH1" <-> "NH2" Residue "19 ARG 47": "NH1" <-> "NH2" Residue "19 ARG 69": "NH1" <-> "NH2" Residue "20 ARG 21": "NH1" <-> "NH2" Residue "20 ARG 68": "NH1" <-> "NH2" Residue "20 ARG 78": "NH1" <-> "NH2" Residue "20 ARG 79": "NH1" <-> "NH2" Residue "20 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 88": "NH1" <-> "NH2" Residue "21 ARG 95": "NH1" <-> "NH2" Residue "21 ARG 110": "NH1" <-> "NH2" Residue "22 ARG 73": "NH1" <-> "NH2" Residue "23 ARG 5": "NH1" <-> "NH2" Residue "23 ARG 6": "NH1" <-> "NH2" Residue "23 ARG 81": "NH1" <-> "NH2" Residue "23 ARG 85": "NH1" <-> "NH2" Residue "23 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "23 ARG 93": "NH1" <-> "NH2" Residue "24 TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "27 ARG 29": "NH1" <-> "NH2" Residue "27 ARG 47": "NH1" <-> "NH2" Residue "27 ARG 52": "NH1" <-> "NH2" Residue "28 ARG 10": "NH1" <-> "NH2" Residue "28 ARG 29": "NH1" <-> "NH2" Residue "28 ARG 44": "NH1" <-> "NH2" Residue "29 ARG 49": "NH1" <-> "NH2" Residue "29 ARG 56": "NH1" <-> "NH2" Residue "30 ARG 9": "NH1" <-> "NH2" Residue "30 ARG 15": "NH1" <-> "NH2" Residue "30 ARG 39": "NH1" <-> "NH2" Residue "30 ARG 51": "NH1" <-> "NH2" Residue "31 ARG 43": "NH1" <-> "NH2" Residue "32 ARG 3": "NH1" <-> "NH2" Residue "32 ARG 12": "NH1" <-> "NH2" Residue "32 ARG 14": "NH1" <-> "NH2" Residue "32 ARG 19": "NH1" <-> "NH2" Residue "32 ARG 21": "NH1" <-> "NH2" Residue "32 ARG 33": "NH1" <-> "NH2" Residue "32 ARG 41": "NH1" <-> "NH2" Residue "33 ARG 12": "NH1" <-> "NH2" Residue "33 ARG 29": "NH1" <-> "NH2" Residue "33 ARG 39": "NH1" <-> "NH2" Residue "33 ARG 41": "NH1" <-> "NH2" Residue "34 ARG 12": "NH1" <-> "NH2" Residue "34 ARG 24": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "Q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "03 ARG 7": "NH1" <-> "NH2" Residue "03 ARG 12": "NH1" <-> "NH2" Residue "03 ARG 162": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z ARG 223": "NH1" <-> "NH2" Residue "Z ARG 269": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153717 Number of models: 1 Model: "" Number of chains: 60 Chain: "04" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "05" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "06" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "07" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "08" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "09" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "10" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 989 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "11" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "12" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "13" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "14" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "15" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "16" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "17" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "18" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "19" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "20" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "21" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "22" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "23" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "24" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "25" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "26" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "27" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "28" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "29" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "30" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "31" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "32" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "33" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "34" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "C" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "G" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "M" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "S" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "U" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "03" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "A" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 92, 'rna2p_pyr': 46, 'rna3p_pur': 782, 'rna3p_pyr': 619} Link IDs: {'rna2p': 138, 'rna3p': 1400} Chain: "01" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 206, 'rna2p_pyr': 91, 'rna3p_pur': 1468, 'rna3p_pyr': 1138} Link IDs: {'rna2p': 297, 'rna3p': 2605} Chain: "02" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 62, 'rna3p_pyr': 53} Link IDs: {'rna2p': 5, 'rna3p': 114} Chain: "X" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "V" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 373 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 15} Chain: "W" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "Y" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1618 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p': 1, 'rna3p_pur': 29, 'rna3p_pyr': 32} Link IDs: {'rna2p': 13, 'rna3p': 62} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "Z" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3061 Unusual residues: {'GCP': 1} Inner-chain residues flagged as termini: ['pdbres="LEU Z 392 "'] Classifications: {'peptide': 392, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 371, None: 1} Not linked: pdbres="LEU Z 392 " pdbres="GCP Z 401 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 57.25, per 1000 atoms: 0.37 Number of scatterers: 153717 At special positions: 0 Unit cell: (277.98, 266.5, 239.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 172 16.00 P 4806 15.00 O 42488 8.00 N 28568 7.00 C 77683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.75 Conformation dependent library (CDL) restraints added in 7.0 seconds 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11882 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 197 helices and 76 sheets defined 38.2% alpha, 18.2% beta 1380 base pairs and 2933 stacking pairs defined. Time for finding SS restraints: 76.55 Creating SS restraints... Processing helix chain '04' and resid 11 through 16 removed outlier: 3.977A pdb=" N VAL04 15 " --> pdb=" O GLY04 11 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL04 16 " --> pdb=" O ARG04 12 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 11 through 16' Processing helix chain '04' and resid 29 through 34 removed outlier: 4.294A pdb=" N LEU04 33 " --> pdb=" O PHE04 29 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLU04 34 " --> pdb=" O ALA04 30 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 29 through 34' Processing helix chain '04' and resid 130 through 135 removed outlier: 3.878A pdb=" N ILE04 134 " --> pdb=" O PRO04 130 " (cutoff:3.500A) Proline residue: 04 135 - end of helix No H-bonds generated for 'chain '04' and resid 130 through 135' Processing helix chain '04' and resid 206 through 214 removed outlier: 4.081A pdb=" N ALA04 210 " --> pdb=" O LYS04 206 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG04 213 " --> pdb=" O ALA04 209 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY04 214 " --> pdb=" O ALA04 210 " (cutoff:3.500A) Processing helix chain '04' and resid 220 through 225 removed outlier: 3.675A pdb=" N MET04 224 " --> pdb=" O ARG04 220 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASN04 225 " --> pdb=" O GLY04 221 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 220 through 225' Processing helix chain '04' and resid 259 through 267 removed outlier: 6.067A pdb=" N ASP04 263 " --> pdb=" O ASN04 259 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS04 264 " --> pdb=" O LYS04 260 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE04 265 " --> pdb=" O ARG04 261 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE04 266 " --> pdb=" O THR04 262 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL04 267 " --> pdb=" O ASP04 263 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 259 through 267' Processing helix chain '05' and resid 61 through 72 removed outlier: 3.639A pdb=" N HIS05 67 " --> pdb=" O PRO05 63 " (cutoff:3.500A) Processing helix chain '05' and resid 120 through 125 Processing helix chain '05' and resid 97 through 102 removed outlier: 4.359A pdb=" N LEU05 100 " --> pdb=" O SER05 97 " (cutoff:3.500A) Processing helix chain '06' and resid 24 through 40 removed outlier: 3.530A pdb=" N VAL06 28 " --> pdb=" O ASN06 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN06 30 " --> pdb=" O ALA06 26 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY06 38 " --> pdb=" O ALA06 34 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG06 40 " --> pdb=" O ALA06 36 " (cutoff:3.500A) Processing helix chain '06' and resid 48 through 53 removed outlier: 6.649A pdb=" N THR06 53 " --> pdb=" O ARG06 49 " (cutoff:3.500A) Processing helix chain '06' and resid 97 through 116 removed outlier: 3.883A pdb=" N VAL06 113 " --> pdb=" O LEU06 109 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG06 114 " --> pdb=" O SER06 110 " (cutoff:3.500A) Processing helix chain '06' and resid 130 through 142 removed outlier: 3.567A pdb=" N ALA06 142 " --> pdb=" O LEU06 138 " (cutoff:3.500A) Processing helix chain '06' and resid 154 through 163 removed outlier: 4.125A pdb=" N ALA06 160 " --> pdb=" O ASN06 156 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA06 161 " --> pdb=" O LEU06 157 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG06 162 " --> pdb=" O PHE06 158 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASN06 163 " --> pdb=" O LEU06 159 " (cutoff:3.500A) Processing helix chain '06' and resid 176 through 183 Processing helix chain '06' and resid 189 through 201 removed outlier: 3.742A pdb=" N GLN06 195 " --> pdb=" O ASP06 191 " (cutoff:3.500A) Processing helix chain '06' and resid 15 through 20 removed outlier: 3.572A pdb=" N GLY06 20 " --> pdb=" O SER06 15 " (cutoff:3.500A) No H-bonds generated for 'chain '06' and resid 15 through 20' Processing helix chain '07' and resid 1 through 20 removed outlier: 3.734A pdb=" N ASP07 5 " --> pdb=" O ALA07 1 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL07 12 " --> pdb=" O LYS07 8 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR07 17 " --> pdb=" O LYS07 13 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU07 18 " --> pdb=" O LYS07 14 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE07 19 " --> pdb=" O LEU07 15 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN07 20 " --> pdb=" O MET07 16 " (cutoff:3.500A) Processing helix chain '07' and resid 45 through 61 removed outlier: 4.051A pdb=" N LEU07 49 " --> pdb=" O ASP07 45 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP07 50 " --> pdb=" O LYS07 46 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY07 61 " --> pdb=" O ALA07 57 " (cutoff:3.500A) Processing helix chain '07' and resid 92 through 110 removed outlier: 4.454A pdb=" N TRP07 96 " --> pdb=" O GLY07 92 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE07 105 " --> pdb=" O ARG07 101 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL07 107 " --> pdb=" O ILE07 103 " (cutoff:3.500A) Proline residue: 07 108 - end of helix Processing helix chain '07' and resid 161 through 171 removed outlier: 3.715A pdb=" N LEU07 168 " --> pdb=" O GLU07 164 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA07 171 " --> pdb=" O ALA07 167 " (cutoff:3.500A) Processing helix chain '07' and resid 23 through 28 removed outlier: 3.882A pdb=" N VAL07 27 " --> pdb=" O VAL07 24 " (cutoff:3.500A) Proline residue: 07 28 - end of helix Processing helix chain '07' and resid 133 through 138 removed outlier: 4.598A pdb=" N ILE07 136 " --> pdb=" O GLU07 133 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE07 137 " --> pdb=" O GLN07 134 " (cutoff:3.500A) Proline residue: 07 138 - end of helix No H-bonds generated for 'chain '07' and resid 133 through 138' Processing helix chain '08' and resid 1 through 7 removed outlier: 4.152A pdb=" N ALA08 6 " --> pdb=" O ARG08 2 " (cutoff:3.500A) Proline residue: 08 7 - end of helix Processing helix chain '08' and resid 59 through 80 removed outlier: 3.694A pdb=" N ALA08 69 " --> pdb=" O GLY08 65 " (cutoff:3.500A) Processing helix chain '08' and resid 136 through 152 removed outlier: 3.523A pdb=" N ILE08 140 " --> pdb=" O ASP08 136 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG08 151 " --> pdb=" O LEU08 147 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG08 152 " --> pdb=" O ARG08 148 " (cutoff:3.500A) Processing helix chain '09' and resid 22 through 28 removed outlier: 3.626A pdb=" N ALA09 26 " --> pdb=" O LYS09 22 " (cutoff:3.500A) Processing helix chain '09' and resid 29 through 34 Processing helix chain '09' and resid 40 through 49 removed outlier: 4.492A pdb=" N ILE09 44 " --> pdb=" O THR09 40 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU09 45 " --> pdb=" O LYS09 41 " (cutoff:3.500A) Processing helix chain '09' and resid 53 through 74 removed outlier: 5.225A pdb=" N LYS09 57 " --> pdb=" O GLU09 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU09 58 " --> pdb=" O LEU09 54 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU09 60 " --> pdb=" O ALA09 56 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU09 62 " --> pdb=" O LEU09 58 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU09 70 " --> pdb=" O ASN09 66 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS09 71 " --> pdb=" O ALA09 67 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE09 72 " --> pdb=" O ARG09 68 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN09 73 " --> pdb=" O ALA09 69 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA09 74 " --> pdb=" O GLU09 70 " (cutoff:3.500A) Processing helix chain '09' and resid 95 through 107 removed outlier: 3.576A pdb=" N THR09 104 " --> pdb=" O ALA09 100 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA09 105 " --> pdb=" O ASP09 101 " (cutoff:3.500A) Processing helix chain '10' and resid 3 through 21 removed outlier: 3.777A pdb=" N GLU10 17 " --> pdb=" O ALA10 13 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS10 20 " --> pdb=" O SER10 16 " (cutoff:3.500A) Processing helix chain '10' and resid 33 through 48 removed outlier: 3.550A pdb=" N GLU10 40 " --> pdb=" O ASP10 36 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG10 42 " --> pdb=" O MET10 38 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA10 48 " --> pdb=" O ALA10 44 " (cutoff:3.500A) Processing helix chain '10' and resid 62 through 71 removed outlier: 3.753A pdb=" N GLY10 66 " --> pdb=" O ARG10 62 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR10 67 " --> pdb=" O ALA10 63 " (cutoff:3.500A) Proline residue: 10 68 - end of helix removed outlier: 4.380A pdb=" N CYS10 71 " --> pdb=" O THR10 67 " (cutoff:3.500A) No H-bonds generated for 'chain '10' and resid 62 through 71' Processing helix chain '10' and resid 72 through 79 removed outlier: 4.713A pdb=" N PHE10 76 " --> pdb=" O LEU10 72 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL10 77 " --> pdb=" O LYS10 73 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY10 78 " --> pdb=" O ASP10 74 " (cutoff:3.500A) Proline residue: 10 79 - end of helix No H-bonds generated for 'chain '10' and resid 72 through 79' Processing helix chain '10' and resid 94 through 106 removed outlier: 3.948A pdb=" N GLU10 98 " --> pdb=" O ARG10 94 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE10 99 " --> pdb=" O LEU10 95 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA10 100 " --> pdb=" O PHE10 96 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA10 102 " --> pdb=" O GLU10 98 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN10 103 " --> pdb=" O PHE10 99 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA10 104 " --> pdb=" O ALA10 100 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS10 105 " --> pdb=" O LYS10 101 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE10 106 " --> pdb=" O ALA10 102 " (cutoff:3.500A) Processing helix chain '11' and resid 23 through 31 removed outlier: 3.745A pdb=" N LEU11 27 " --> pdb=" O VAL11 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN11 29 " --> pdb=" O PRO11 25 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLN11 30 " --> pdb=" O ALA11 26 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY11 31 " --> pdb=" O LEU11 27 " (cutoff:3.500A) Processing helix chain '11' and resid 33 through 46 removed outlier: 3.560A pdb=" N PHE11 41 " --> pdb=" O PHE11 37 " (cutoff:3.500A) Processing helix chain '11' and resid 74 through 83 removed outlier: 3.775A pdb=" N LYS11 81 " --> pdb=" O VAL11 77 " (cutoff:3.500A) Processing helix chain '11' and resid 104 through 113 removed outlier: 3.709A pdb=" N ILE11 108 " --> pdb=" O GLN11 104 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR11 111 " --> pdb=" O GLU11 107 " (cutoff:3.500A) Processing helix chain '11' and resid 120 through 136 removed outlier: 3.785A pdb=" N SER11 127 " --> pdb=" O ALA11 123 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY11 136 " --> pdb=" O ALA11 132 " (cutoff:3.500A) Processing helix chain '12' and resid 24 through 38 removed outlier: 3.532A pdb=" N GLU12 31 " --> pdb=" O ARG12 27 " (cutoff:3.500A) Processing helix chain '12' and resid 67 through 72 removed outlier: 3.520A pdb=" N LYS12 72 " --> pdb=" O LYS12 68 " (cutoff:3.500A) Processing helix chain '12' and resid 88 through 96 Processing helix chain '12' and resid 97 through 110 removed outlier: 5.012A pdb=" N ILE12 101 " --> pdb=" O PRO12 97 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS12 106 " --> pdb=" O GLU12 102 " (cutoff:3.500A) Proline residue: 12 110 - end of helix Processing helix chain '12' and resid 112 through 123 removed outlier: 3.838A pdb=" N LYS12 121 " --> pdb=" O ALA12 117 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU12 122 " --> pdb=" O MET12 118 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LYS12 123 " --> pdb=" O PHE12 119 " (cutoff:3.500A) Processing helix chain '13' and resid 110 through 119 removed outlier: 5.077A pdb=" N LYS13 114 " --> pdb=" O GLU13 110 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE13 115 " --> pdb=" O LYS13 111 " (cutoff:3.500A) Processing helix chain '14' and resid 37 through 42 removed outlier: 5.069A pdb=" N ARG14 41 " --> pdb=" O GLY14 37 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER14 42 " --> pdb=" O GLN14 38 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 37 through 42' Processing helix chain '14' and resid 56 through 62 Proline residue: 14 62 - end of helix Processing helix chain '14' and resid 68 through 75 removed outlier: 3.643A pdb=" N ALA14 72 " --> pdb=" O SER14 68 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE14 73 " --> pdb=" O ARG14 69 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR14 74 " --> pdb=" O LYS14 70 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ALA14 75 " --> pdb=" O ALA14 71 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 68 through 75' Processing helix chain '14' and resid 78 through 87 removed outlier: 3.853A pdb=" N LEU14 82 " --> pdb=" O ARG14 78 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA14 83 " --> pdb=" O LEU14 79 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS14 84 " --> pdb=" O SER14 80 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL14 85 " --> pdb=" O ASP14 81 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLU14 86 " --> pdb=" O LEU14 82 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLY14 87 " --> pdb=" O ALA14 83 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 78 through 87' Processing helix chain '14' and resid 91 through 99 removed outlier: 4.496A pdb=" N LEU14 95 " --> pdb=" O ASP14 91 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS14 96 " --> pdb=" O LEU14 92 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA14 97 " --> pdb=" O ASN14 93 " (cutoff:3.500A) Processing helix chain '14' and resid 128 through 139 removed outlier: 5.795A pdb=" N ARG14 132 " --> pdb=" O THR14 128 " (cutoff:3.500A) Processing helix chain '15' and resid 42 through 58 removed outlier: 3.712A pdb=" N ALA15 52 " --> pdb=" O ALA15 48 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL15 57 " --> pdb=" O MET15 53 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS15 58 " --> pdb=" O THR15 54 " (cutoff:3.500A) Processing helix chain '15' and resid 109 through 125 removed outlier: 3.931A pdb=" N LYS15 118 " --> pdb=" O ARG15 114 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU15 119 " --> pdb=" O GLU15 115 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS15 123 " --> pdb=" O LEU15 119 " (cutoff:3.500A) Proline residue: 15 125 - end of helix Processing helix chain '16' and resid 13 through 32 removed outlier: 3.609A pdb=" N GLY16 26 " --> pdb=" O ARG16 22 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER16 27 " --> pdb=" O ASN16 23 " (cutoff:3.500A) Processing helix chain '16' and resid 37 through 58 removed outlier: 3.741A pdb=" N ARG16 45 " --> pdb=" O ALA16 41 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ARG16 46 " --> pdb=" O LYS16 42 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL16 47 " --> pdb=" O GLU16 43 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU16 49 " --> pdb=" O ARG16 45 " (cutoff:3.500A) Proline residue: 16 50 - end of helix removed outlier: 4.195A pdb=" N THR16 57 " --> pdb=" O THR16 53 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASP16 58 " --> pdb=" O LEU16 54 " (cutoff:3.500A) Processing helix chain '16' and resid 59 through 71 removed outlier: 4.369A pdb=" N ARG16 63 " --> pdb=" O SER16 59 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG16 69 " --> pdb=" O LEU16 65 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR16 70 " --> pdb=" O ALA16 66 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG16 71 " --> pdb=" O PHE16 67 " (cutoff:3.500A) Processing helix chain '16' and resid 72 through 88 removed outlier: 4.408A pdb=" N PHE16 80 " --> pdb=" O VAL16 76 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN16 81 " --> pdb=" O ALA16 77 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU16 83 " --> pdb=" O LEU16 79 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY16 84 " --> pdb=" O PHE16 80 " (cutoff:3.500A) Proline residue: 16 85 - end of helix removed outlier: 4.481A pdb=" N ALA16 88 " --> pdb=" O GLY16 84 " (cutoff:3.500A) Processing helix chain '17' and resid 2 through 20 removed outlier: 3.650A pdb=" N ARG17 7 " --> pdb=" O LYS17 3 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG17 13 " --> pdb=" O ARG17 9 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA17 14 " --> pdb=" O ARG17 10 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU17 18 " --> pdb=" O ALA17 14 " (cutoff:3.500A) Processing helix chain '17' and resid 55 through 63 removed outlier: 4.609A pdb=" N GLN17 61 " --> pdb=" O ALA17 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU17 62 " --> pdb=" O ILE17 58 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS17 63 " --> pdb=" O ALA17 59 " (cutoff:3.500A) Processing helix chain '17' and resid 67 through 86 removed outlier: 3.767A pdb=" N GLU17 84 " --> pdb=" O GLU17 80 " (cutoff:3.500A) Processing helix chain '17' and resid 101 through 114 removed outlier: 3.771A pdb=" N GLY17 114 " --> pdb=" O ALA17 110 " (cutoff:3.500A) Processing helix chain '18' and resid 1 through 13 removed outlier: 3.546A pdb=" N LEU18 7 " --> pdb=" O ILE18 3 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU18 10 " --> pdb=" O GLN18 6 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN18 11 " --> pdb=" O LEU18 7 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET18 12 " --> pdb=" O GLU18 8 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LYS18 13 " --> pdb=" O GLN18 9 " (cutoff:3.500A) Processing helix chain '18' and resid 96 through 103 removed outlier: 4.978A pdb=" N ARG18 100 " --> pdb=" O LEU18 96 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLU18 101 " --> pdb=" O TYR18 97 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR18 103 " --> pdb=" O LEU18 99 " (cutoff:3.500A) Processing helix chain '19' and resid 5 through 21 removed outlier: 3.560A pdb=" N GLN19 19 " --> pdb=" O LYS19 15 " (cutoff:3.500A) Processing helix chain '19' and resid 25 through 30 removed outlier: 3.848A pdb=" N ARG19 29 " --> pdb=" O GLY19 25 " (cutoff:3.500A) Processing helix chain '19' and resid 38 through 60 removed outlier: 3.577A pdb=" N ARG19 49 " --> pdb=" O ALA19 45 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG19 50 " --> pdb=" O TYR19 46 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS19 53 " --> pdb=" O ARG19 49 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG19 54 " --> pdb=" O ARG19 50 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG19 57 " --> pdb=" O LYS19 53 " (cutoff:3.500A) Processing helix chain '19' and resid 62 through 72 Processing helix chain '19' and resid 74 through 86 Processing helix chain '19' and resid 90 through 101 removed outlier: 3.888A pdb=" N ASP19 96 " --> pdb=" O LYS19 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL19 99 " --> pdb=" O ALA19 95 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE19 100 " --> pdb=" O ASP19 96 " (cutoff:3.500A) Processing helix chain '19' and resid 102 through 117 Processing helix chain '21' and resid 13 through 25 removed outlier: 3.572A pdb=" N LEU21 19 " --> pdb=" O GLN21 15 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL21 20 " --> pdb=" O LYS21 16 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU21 23 " --> pdb=" O LEU21 19 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE21 24 " --> pdb=" O VAL21 20 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ARG21 25 " --> pdb=" O ALA21 21 " (cutoff:3.500A) Processing helix chain '21' and resid 28 through 39 removed outlier: 3.580A pdb=" N ASP21 34 " --> pdb=" O SER21 30 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE21 35 " --> pdb=" O GLN21 31 " (cutoff:3.500A) Processing helix chain '21' and resid 41 through 62 Processing helix chain '22' and resid 2 through 11 removed outlier: 3.983A pdb=" N LYS22 9 " --> pdb=" O GLU22 5 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU22 11 " --> pdb=" O LEU22 7 " (cutoff:3.500A) Processing helix chain '22' and resid 17 through 26 Processing helix chain '22' and resid 39 through 50 Processing helix chain '23' and resid 65 through 70 removed outlier: 4.073A pdb=" N VAL23 69 " --> pdb=" O GLN23 65 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA23 70 " --> pdb=" O VAL23 66 " (cutoff:3.500A) No H-bonds generated for 'chain '23' and resid 65 through 70' Processing helix chain '24' and resid 13 through 24 removed outlier: 4.294A pdb=" N ASN24 24 " --> pdb=" O LEU24 20 " (cutoff:3.500A) Processing helix chain '24' and resid 43 through 53 removed outlier: 4.505A pdb=" N VAL24 47 " --> pdb=" O ASP24 43 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA24 52 " --> pdb=" O MET24 48 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYS24 53 " --> pdb=" O ASN24 49 " (cutoff:3.500A) Processing helix chain '24' and resid 54 through 59 removed outlier: 3.611A pdb=" N SER24 58 " --> pdb=" O ALA24 54 " (cutoff:3.500A) Processing helix chain '26' and resid 51 through 61 removed outlier: 3.752A pdb=" N ARG26 56 " --> pdb=" O ALA26 52 " (cutoff:3.500A) Processing helix chain '26' and resid 62 through 74 Processing helix chain '27' and resid 1 through 8 removed outlier: 3.874A pdb=" N LEU27 6 " --> pdb=" O LYS27 2 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG27 7 " --> pdb=" O ALA27 3 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU27 8 " --> pdb=" O LYS27 4 " (cutoff:3.500A) Processing helix chain '27' and resid 9 through 23 Processing helix chain '27' and resid 25 through 35 removed outlier: 3.759A pdb=" N ARG27 29 " --> pdb=" O GLN27 25 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER27 34 " --> pdb=" O MET27 30 " (cutoff:3.500A) Processing helix chain '27' and resid 40 through 63 removed outlier: 3.563A pdb=" N VAL27 46 " --> pdb=" O LEU27 42 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG27 48 " --> pdb=" O LYS27 44 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY27 62 " --> pdb=" O ASN27 58 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ALA27 63 " --> pdb=" O GLU27 59 " (cutoff:3.500A) Processing helix chain '28' and resid 16 through 27 Processing helix chain '28' and resid 40 through 51 removed outlier: 3.847A pdb=" N MET28 46 " --> pdb=" O ALA28 42 " (cutoff:3.500A) Processing helix chain '29' and resid 43 through 51 removed outlier: 3.603A pdb=" N LYS29 47 " --> pdb=" O PHE29 43 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLN29 48 " --> pdb=" O PHE29 44 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL29 51 " --> pdb=" O LYS29 47 " (cutoff:3.500A) Processing helix chain '29' and resid 55 through 65 removed outlier: 4.229A pdb=" N ARG29 59 " --> pdb=" O GLY29 55 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG29 63 " --> pdb=" O ARG29 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE29 64 " --> pdb=" O PHE29 60 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN29 65 " --> pdb=" O ASN29 61 " (cutoff:3.500A) Processing helix chain '30' and resid 8 through 18 removed outlier: 4.977A pdb=" N HIS30 18 " --> pdb=" O MET30 14 " (cutoff:3.500A) Processing helix chain '31' and resid 25 through 30 Proline residue: 31 30 - end of helix Processing helix chain '32' and resid 8 through 16 Processing helix chain '32' and resid 17 through 24 removed outlier: 4.782A pdb=" N THR32 24 " --> pdb=" O ALA32 20 " (cutoff:3.500A) Processing helix chain '32' and resid 25 through 38 Processing helix chain '33' and resid 6 through 13 removed outlier: 3.989A pdb=" N LYS33 11 " --> pdb=" O ARG33 7 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG33 12 " --> pdb=" O GLY33 8 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE33 13 " --> pdb=" O ALA33 9 " (cutoff:3.500A) Processing helix chain '33' and resid 31 through 36 removed outlier: 5.017A pdb=" N LYS33 35 " --> pdb=" O ILE33 31 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA33 36 " --> pdb=" O LEU33 32 " (cutoff:3.500A) No H-bonds generated for 'chain '33' and resid 31 through 36' Processing helix chain '33' and resid 37 through 45 Proline residue: 33 45 - end of helix Processing helix chain '33' and resid 50 through 62 removed outlier: 4.471A pdb=" N GLY33 55 " --> pdb=" O LYS33 51 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU33 56 " --> pdb=" O GLY33 52 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL33 57 " --> pdb=" O ASP33 53 " (cutoff:3.500A) Proline residue: 33 62 - end of helix Processing helix chain 'B' and resid 43 through 63 Proline residue: B 47 - end of helix removed outlier: 3.743A pdb=" N ASN B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 removed outlier: 5.847A pdb=" N SER B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLU B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 122 removed outlier: 3.622A pdb=" N VAL B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.517A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 4.388A pdb=" N MET B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 154' Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.661A pdb=" N ILE B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLY B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 225 removed outlier: 4.015A pdb=" N TYR B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 removed outlier: 3.816A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.604A pdb=" N VAL C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 80 through 95 Processing helix chain 'C' and resid 107 through 112 removed outlier: 5.491A pdb=" N ALA C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.670A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 removed outlier: 3.544A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 3.773A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.690A pdb=" N TYR D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.957A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 4.048A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 109 through 120 removed outlier: 4.320A pdb=" N LYS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 165 removed outlier: 6.978A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 4.647A pdb=" N SER D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.039A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 removed outlier: 3.736A pdb=" N LYS E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 5.766A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E 114 " --> pdb=" O MET E 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 146 removed outlier: 3.525A pdb=" N ARG E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 156 removed outlier: 3.532A pdb=" N ALA E 154 " --> pdb=" O GLU E 150 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS E 155 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 165 removed outlier: 3.868A pdb=" N LEU E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 33 Proline residue: F 19 - end of helix removed outlier: 3.715A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.584A pdb=" N LEU F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN F 81 " --> pdb=" O THR F 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 removed outlier: 3.540A pdb=" N PHE G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 54 Processing helix chain 'G' and resid 56 through 69 removed outlier: 3.748A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 110 removed outlier: 3.641A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 removed outlier: 3.677A pdb=" N GLU G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 148 removed outlier: 3.866A pdb=" N LYS G 135 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL G 140 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU G 145 " --> pdb=" O HIS G 141 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 20 Processing helix chain 'H' and resid 29 through 43 removed outlier: 3.925A pdb=" N VAL H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.514A pdb=" N ARG H 116 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 38 Processing helix chain 'I' and resid 44 through 52 removed outlier: 4.555A pdb=" N ARG I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Proline residue: I 50 - end of helix Processing helix chain 'I' and resid 70 through 87 removed outlier: 4.926A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 101 removed outlier: 4.236A pdb=" N ARG I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 30 removed outlier: 4.190A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.976A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 Processing helix chain 'K' and resid 53 through 59 removed outlier: 3.669A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 59 - end of helix No H-bonds generated for 'chain 'K' and resid 53 through 59' Processing helix chain 'K' and resid 60 through 77 removed outlier: 3.509A pdb=" N ASP K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ALA K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLU K 75 " --> pdb=" O ASP K 71 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 removed outlier: 5.700A pdb=" N THR K 95 " --> pdb=" O GLY K 91 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 Proline residue: L 10 - end of helix Processing helix chain 'L' and resid 112 through 117 removed outlier: 4.641A pdb=" N TYR L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 112 through 117' Processing helix chain 'M' and resid 13 through 21 removed outlier: 3.655A pdb=" N THR M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.583A pdb=" N LEU M 33 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA M 36 " --> pdb=" O ILE M 32 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 48 removed outlier: 5.252A pdb=" N SER M 48 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 63 removed outlier: 3.879A pdb=" N ASP M 53 " --> pdb=" O GLU M 49 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N PHE M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL M 63 " --> pdb=" O VAL M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 83 removed outlier: 3.556A pdb=" N GLY M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 93 Processing helix chain 'M' and resid 105 through 110 removed outlier: 3.594A pdb=" N GLY M 110 " --> pdb=" O ARG M 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 20 removed outlier: 3.506A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 29 removed outlier: 4.942A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 50 removed outlier: 3.806A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 removed outlier: 4.350A pdb=" N GLN N 59 " --> pdb=" O SER N 55 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ARG N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 55 through 60' Processing helix chain 'N' and resid 79 through 90 removed outlier: 3.583A pdb=" N ARG N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 14 removed outlier: 3.653A pdb=" N ALA O 8 " --> pdb=" O THR O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 43 removed outlier: 3.562A pdb=" N VAL O 28 " --> pdb=" O THR O 24 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA O 29 " --> pdb=" O GLU O 25 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 73 Processing helix chain 'O' and resid 74 through 83 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 79 Processing helix chain 'R' and resid 12 through 17 removed outlier: 3.890A pdb=" N GLY R 16 " --> pdb=" O PHE R 12 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL R 17 " --> pdb=" O THR R 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 12 through 17' Processing helix chain 'R' and resid 24 through 33 removed outlier: 4.160A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.524A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 65 Processing helix chain 'S' and resid 11 through 25 removed outlier: 3.890A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 75 removed outlier: 3.963A pdb=" N PHE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) Proline residue: S 75 - end of helix Processing helix chain 'S' and resid 41 through 46 removed outlier: 4.922A pdb=" N GLY S 45 " --> pdb=" O ASN S 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 41 removed outlier: 4.759A pdb=" N ARG T 9 " --> pdb=" O SER T 5 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA T 40 " --> pdb=" O ALA T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 Proline residue: T 55 - end of helix removed outlier: 3.591A pdb=" N ASP T 58 " --> pdb=" O GLN T 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG T 59 " --> pdb=" O PRO T 55 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA T 61 " --> pdb=" O VAL T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 86 removed outlier: 5.595A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA T 72 " --> pdb=" O LYS T 68 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU T 78 " --> pdb=" O HIS T 74 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU T 85 " --> pdb=" O GLN T 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 23 removed outlier: 4.115A pdb=" N ARG U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 33 removed outlier: 5.470A pdb=" N LEU U 28 " --> pdb=" O LYS U 24 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG U 32 " --> pdb=" O LEU U 28 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 61 Proline residue: U 40 - end of helix removed outlier: 3.612A pdb=" N LYS U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) Processing helix chain '03' and resid 5 through 16 removed outlier: 3.795A pdb=" N VAL03 10 " --> pdb=" O LYS03 6 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL03 15 " --> pdb=" O ILE03 11 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP03 16 " --> pdb=" O ARG03 12 " (cutoff:3.500A) Processing helix chain '03' and resid 22 through 35 removed outlier: 4.331A pdb=" N ILE03 27 " --> pdb=" O ILE03 23 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA03 28 " --> pdb=" O ASN03 24 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU03 29 " --> pdb=" O GLU03 25 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU03 30 " --> pdb=" O ALA03 26 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LYS03 31 " --> pdb=" O ILE03 27 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU03 32 " --> pdb=" O ALA03 28 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR03 35 " --> pdb=" O LYS03 31 " (cutoff:3.500A) Processing helix chain '03' and resid 181 through 200 removed outlier: 3.530A pdb=" N ALA03 191 " --> pdb=" O GLU03 187 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA03 195 " --> pdb=" O ALA03 191 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS03 200 " --> pdb=" O LEU03 196 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 39 removed outlier: 3.742A pdb=" N ALA Z 30 " --> pdb=" O THR Z 26 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR Z 32 " --> pdb=" O THR Z 28 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU Z 35 " --> pdb=" O ILE Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 51 removed outlier: 4.910A pdb=" N ASN Z 51 " --> pdb=" O ASP Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 59 Processing helix chain 'Z' and resid 84 through 97 removed outlier: 3.557A pdb=" N VAL Z 88 " --> pdb=" O HIS Z 84 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LYS Z 89 " --> pdb=" O ALA Z 85 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN Z 90 " --> pdb=" O ASP Z 86 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA Z 96 " --> pdb=" O ILE Z 92 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 126 removed outlier: 3.792A pdb=" N LEU Z 121 " --> pdb=" O GLU Z 117 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY Z 122 " --> pdb=" O HIS Z 118 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG Z 123 " --> pdb=" O ILE Z 119 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN Z 124 " --> pdb=" O LEU Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 136 through 141 removed outlier: 4.058A pdb=" N VAL Z 140 " --> pdb=" O LYS Z 136 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP Z 141 " --> pdb=" O CYS Z 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 136 through 141' Processing helix chain 'Z' and resid 142 through 161 removed outlier: 3.515A pdb=" N LEU Z 146 " --> pdb=" O ASP Z 142 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU Z 148 " --> pdb=" O GLU Z 144 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL Z 149 " --> pdb=" O LEU Z 145 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG Z 154 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 163 through 168 removed outlier: 4.179A pdb=" N THR Z 167 " --> pdb=" O PRO Z 163 " (cutoff:3.500A) Proline residue: Z 168 - end of helix No H-bonds generated for 'chain 'Z' and resid 163 through 168' Processing helix chain 'Z' and resid 173 through 180 removed outlier: 3.856A pdb=" N ALA Z 177 " --> pdb=" O SER Z 173 " (cutoff:3.500A) Processing helix chain 'Z' and resid 181 through 198 removed outlier: 3.763A pdb=" N LEU Z 191 " --> pdb=" O LYS Z 187 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP Z 196 " --> pdb=" O ALA Z 192 " (cutoff:3.500A) Processing helix chain 'Z' and resid 282 through 287 removed outlier: 4.155A pdb=" N ILE Z 286 " --> pdb=" O LYS Z 282 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU Z 287 " --> pdb=" O ARG Z 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 282 through 287' Processing sheet with id= 1, first strand: chain '04' and resid 79 through 82 removed outlier: 6.994A pdb=" N LEU04 92 " --> pdb=" O GLU04 78 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP04 113 " --> pdb=" O VAL04 77 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '04' and resid 137 through 140 removed outlier: 4.191A pdb=" N SER04 138 " --> pdb=" O ILE04 163 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN04 162 " --> pdb=" O ARG04 174 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR04 172 " --> pdb=" O VAL04 164 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU04 179 " --> pdb=" O LEU04 175 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '04' and resid 89 through 95 removed outlier: 5.070A pdb=" N ASN04 89 " --> pdb=" O ALA04 105 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU04 99 " --> pdb=" O TYR04 95 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '05' and resid 3 through 7 removed outlier: 6.696A pdb=" N ASP05 200 " --> pdb=" O THR05 112 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR05 112 " --> pdb=" O ASP05 200 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '05' and resid 11 through 16 removed outlier: 4.451A pdb=" N VAL05 20 " --> pdb=" O THR05 16 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG05 179 " --> pdb=" O LEU05 188 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '05' and resid 32 through 35 removed outlier: 6.326A pdb=" N GLN05 49 " --> pdb=" O THR05 35 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '05' and resid 46 through 51 removed outlier: 5.949A pdb=" N ARG05 46 " --> pdb=" O LEU05 84 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '06' and resid 1 through 6 removed outlier: 3.803A pdb=" N LEU06 12 " --> pdb=" O LEU06 3 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER06 10 " --> pdb=" O LEU06 5 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '06' and resid 117 through 120 removed outlier: 5.716A pdb=" N ARG06 117 " --> pdb=" O ASP06 184 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL06 187 " --> pdb=" O LEU06 147 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE06 149 " --> pdb=" O VAL06 187 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP06 168 " --> pdb=" O VAL06 146 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '07' and resid 64 through 67 removed outlier: 3.506A pdb=" N GLY07 85 " --> pdb=" O THR07 67 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN07 36 " --> pdb=" O ASP07 152 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLY07 38 " --> pdb=" O GLY07 150 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY07 150 " --> pdb=" O GLY07 38 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL07 131 " --> pdb=" O LEU07 151 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '08' and resid 14 through 18 Processing sheet with id= 12, first strand: chain '08' and resid 40 through 44 Processing sheet with id= 13, first strand: chain '08' and resid 81 through 88 removed outlier: 6.138A pdb=" N THR08 128 " --> pdb=" O LEU08 88 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '08' and resid 93 through 97 removed outlier: 3.581A pdb=" N ALA08 96 " --> pdb=" O ASN08 103 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '09' and resid 17 through 20 removed outlier: 4.111A pdb=" N ASP09 17 " --> pdb=" O LEU09 5 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL09 19 " --> pdb=" O VAL09 3 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS09 35 " --> pdb=" O LEU09 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '09' and resid 126 through 133 removed outlier: 4.332A pdb=" N GLY09 126 " --> pdb=" O VAL09 146 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE09 132 " --> pdb=" O ALA09 140 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '10' and resid 24 through 28 removed outlier: 4.358A pdb=" N ALA10 25 " --> pdb=" O SER10 85 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER10 85 " --> pdb=" O ALA10 25 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '11' and resid 5 through 10 removed outlier: 3.550A pdb=" N ILE11 58 " --> pdb=" O VAL11 8 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER11 65 " --> pdb=" O TYR11 61 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '11' and resid 98 through 101 removed outlier: 4.131A pdb=" N ILE11 100 " --> pdb=" O VAL11 138 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '12' and resid 14 through 19 Processing sheet with id= 21, first strand: chain '12' and resid 74 through 78 removed outlier: 7.495A pdb=" N GLY12 83 " --> pdb=" O THR12 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '13' and resid 17 through 21 removed outlier: 6.284A pdb=" N ARG13 17 " --> pdb=" O VAL13 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL13 19 " --> pdb=" O LEU13 8 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR13 6 " --> pdb=" O CYS13 21 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN13 82 " --> pdb=" O MET13 7 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '15' and resid 37 through 40 removed outlier: 3.573A pdb=" N TYR15 91 " --> pdb=" O ILE15 73 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '15' and resid 62 through 65 removed outlier: 3.796A pdb=" N TYR15 103 " --> pdb=" O LEU15 33 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU15 33 " --> pdb=" O LEU15 102 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '15' and resid 30 through 36 removed outlier: 6.936A pdb=" N SER15 30 " --> pdb=" O LYS15 133 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS15 127 " --> pdb=" O VAL15 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '16' and resid 33 through 36 Processing sheet with id= 27, first strand: chain '17' and resid 35 through 41 removed outlier: 4.394A pdb=" N VAL17 28 " --> pdb=" O ASP17 93 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '18' and resid 37 through 45 removed outlier: 6.589A pdb=" N THR18 24 " --> pdb=" O LYS18 86 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '18' and resid 48 through 52 removed outlier: 4.282A pdb=" N ALA18 48 " --> pdb=" O THR18 59 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG18 52 " --> pdb=" O HIS18 55 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N SER18 56 " --> pdb=" O THR18 75 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '20' and resid 11 through 14 removed outlier: 4.389A pdb=" N TYR20 2 " --> pdb=" O ALA20 42 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA20 42 " --> pdb=" O TYR20 2 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '20' and resid 19 through 23 removed outlier: 6.118A pdb=" N ASP20 95 " --> pdb=" O VAL20 64 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS20 60 " --> pdb=" O THR20 99 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU20 31 " --> pdb=" O VAL20 63 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '20' and resid 57 through 60 removed outlier: 3.809A pdb=" N SER20 102 " --> pdb=" O VAL20 58 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '20' and resid 65 through 68 removed outlier: 3.693A pdb=" N GLY20 67 " --> pdb=" O PHE20 93 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '20' and resid 71 through 78 removed outlier: 4.409A pdb=" N TYR20 83 " --> pdb=" O ARG20 78 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '21' and resid 4 through 8 removed outlier: 6.480A pdb=" N VAL21 106 " --> pdb=" O THR21 72 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '21' and resid 74 through 88 No H-bonds generated for sheet with id= 36 Processing sheet with id= 37, first strand: chain '22' and resid 29 through 33 removed outlier: 4.502A pdb=" N LYS22 66 " --> pdb=" O ARG22 77 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP22 79 " --> pdb=" O LYS22 64 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS22 64 " --> pdb=" O ASP22 79 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS22 81 " --> pdb=" O VAL22 62 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL22 62 " --> pdb=" O LYS22 81 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA22 83 " --> pdb=" O THR22 60 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR22 60 " --> pdb=" O ALA22 83 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL22 85 " --> pdb=" O VAL22 58 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL22 58 " --> pdb=" O VAL22 85 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '23' and resid 39 through 43 removed outlier: 4.577A pdb=" N ASN23 39 " --> pdb=" O ALA23 62 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '23' and resid 82 through 85 Processing sheet with id= 40, first strand: chain '24' and resid 69 through 72 removed outlier: 3.750A pdb=" N ILE24 89 " --> pdb=" O PRO24 27 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '25' and resid 33 through 36 removed outlier: 3.602A pdb=" N GLN25 36 " --> pdb=" O HIS25 53 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS25 53 " --> pdb=" O GLN25 36 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR25 54 " --> pdb=" O GLY25 50 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASN25 46 " --> pdb=" O LYS25 58 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '25' and resid 41 through 44 removed outlier: 3.509A pdb=" N HIS25 42 " --> pdb=" O LYS25 74 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE25 78 " --> pdb=" O GLY25 44 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '26' and resid 11 through 15 removed outlier: 3.625A pdb=" N VAL26 12 " --> pdb=" O PHE26 28 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '26' and resid 34 through 40 removed outlier: 3.542A pdb=" N ARG26 44 " --> pdb=" O VAL26 39 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '28' and resid 32 through 38 removed outlier: 4.111A pdb=" N HIS28 33 " --> pdb=" O GLN28 8 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS28 5 " --> pdb=" O GLU28 57 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N MET28 53 " --> pdb=" O THR28 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '29' and resid 20 through 25 removed outlier: 4.170A pdb=" N ASN29 20 " --> pdb=" O CYS29 16 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS29 16 " --> pdb=" O ASN29 20 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '31' and resid 18 through 23 removed outlier: 5.931A pdb=" N HIS31 18 " --> pdb=" O SER31 12 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR31 22 " --> pdb=" O ILE31 8 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE31 47 " --> pdb=" O SER31 13 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR31 48 " --> pdb=" O LEU31 35 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU31 35 " --> pdb=" O TYR31 48 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '33' and resid 21 through 24 removed outlier: 5.689A pdb=" N PHE33 21 " --> pdb=" O VAL33 49 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '34' and resid 23 through 27 removed outlier: 5.584A pdb=" N ILE34 23 " --> pdb=" O GLN34 37 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N CYS34 27 " --> pdb=" O HIS34 33 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N HIS34 33 " --> pdb=" O CYS34 27 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'B' and resid 65 through 70 removed outlier: 4.009A pdb=" N PHE B 183 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL B 162 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE B 197 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 184 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 62 through 70 removed outlier: 3.718A pdb=" N VAL C 65 " --> pdb=" O GLN C 99 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 166 through 169 removed outlier: 7.317A pdb=" N ASP C 180 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'D' and resid 139 through 143 removed outlier: 5.984A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TRP D 169 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'E' and resid 10 through 15 removed outlier: 3.570A pdb=" N GLN E 11 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE E 29 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 16 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'E' and resid 82 through 87 removed outlier: 8.173A pdb=" N HIS E 82 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL E 93 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR E 127 " --> pdb=" O ARG E 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'E' and resid 31 through 40 removed outlier: 4.738A pdb=" N GLY E 50 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'F' and resid 38 through 42 removed outlier: 4.885A pdb=" N ASN F 63 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE F 6 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU F 5 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'G' and resid 72 through 76 Processing sheet with id= 59, first strand: chain 'H' and resid 22 through 28 removed outlier: 6.836A pdb=" N ALA H 22 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'H' and resid 73 through 76 removed outlier: 3.783A pdb=" N SER H 73 " --> pdb=" O ALA H 129 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'I' and resid 4 through 10 removed outlier: 4.309A pdb=" N GLY I 9 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS I 26 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'J' and resid 42 through 52 removed outlier: 5.260A pdb=" N LEU J 71 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU J 47 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE J 67 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE J 8 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE J 6 " --> pdb=" O ILE J 76 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'K' and resid 30 through 35 removed outlier: 3.896A pdb=" N ILE K 30 " --> pdb=" O HIS K 23 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL K 83 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'L' and resid 35 through 40 removed outlier: 4.471A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'L' and resid 80 through 83 removed outlier: 5.002A pdb=" N LEU L 80 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'P' and resid 4 through 10 removed outlier: 5.481A pdb=" N GLN P 18 " --> pdb=" O ALA P 7 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL P 19 " --> pdb=" O GLY P 37 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'Q' and resid 6 through 10 removed outlier: 3.947A pdb=" N GLY Q 9 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Q' and resid 20 through 30 removed outlier: 3.957A pdb=" N LYS Q 35 " --> pdb=" O HIS Q 30 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'S' and resid 47 through 51 removed outlier: 3.847A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '03' and resid 59 through 62 removed outlier: 5.929A pdb=" N VAL03 59 " --> pdb=" O ASN03 165 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '03' and resid 170 through 176 removed outlier: 3.567A pdb=" N THR03 173 " --> pdb=" O VAL03 44 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL03 42 " --> pdb=" O ILE03 175 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS03 211 " --> pdb=" O ASN03 47 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Z' and resid 64 through 70 removed outlier: 3.502A pdb=" N HIS Z 75 " --> pdb=" O PRO Z 10 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLY Z 18 " --> pdb=" O CYS Z 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY Z 100 " --> pdb=" O ASN Z 13 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY Z 15 " --> pdb=" O GLY Z 100 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS Z 19 " --> pdb=" O VAL Z 104 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA Z 106 " --> pdb=" O HIS Z 19 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR Z 129 " --> pdb=" O ASP Z 99 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA Z 101 " --> pdb=" O TYR Z 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU Z 103 " --> pdb=" O ILE Z 131 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL Z 105 " --> pdb=" O PHE Z 133 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Z' and resid 210 through 213 removed outlier: 6.502A pdb=" N PHE Z 210 " --> pdb=" O LYS Z 294 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU Z 240 " --> pdb=" O CYS Z 255 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN Z 251 " --> pdb=" O ILE Z 244 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Z' and resid 215 through 218 removed outlier: 3.644A pdb=" N ASP Z 216 " --> pdb=" O THR Z 228 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR Z 228 " --> pdb=" O ASP Z 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL Z 226 " --> pdb=" O PHE Z 218 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR Z 225 " --> pdb=" O LEU Z 278 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY Z 257 " --> pdb=" O LEU Z 277 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Z' and resid 327 through 331 removed outlier: 3.514A pdb=" N VAL Z 337 " --> pdb=" O PHE Z 330 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Z' and resid 356 through 362 removed outlier: 3.520A pdb=" N PHE Z 304 " --> pdb=" O VAL Z 360 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU Z 362 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR Z 302 " --> pdb=" O LEU Z 362 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU Z 305 " --> pdb=" O ALA Z 389 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU Z 307 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL Z 387 " --> pdb=" O GLU Z 307 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR Z 309 " --> pdb=" O ALA Z 385 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU Z 372 " --> pdb=" O VAL Z 388 " (cutoff:3.500A) 1822 hydrogen bonds defined for protein. 5379 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3400 hydrogen bonds 5616 hydrogen bond angles 0 basepair planarities 1380 basepair parallelities 2933 stacking parallelities Total time for adding SS restraints: 245.65 Time building geometry restraints manager: 64.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 32158 1.34 - 1.46: 65786 1.46 - 1.58: 58921 1.58 - 1.71: 9610 1.71 - 1.83: 305 Bond restraints: 166780 Sorted by residual: bond pdb=" C3B GCP Z 401 " pdb=" PG GCP Z 401 " ideal model delta sigma weight residual 1.871 1.627 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C3B GCP Z 401 " pdb=" PB GCP Z 401 " ideal model delta sigma weight residual 1.807 1.616 0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" O3A GCP Z 401 " pdb=" PB GCP Z 401 " ideal model delta sigma weight residual 1.697 1.533 0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" C5 U8U Y 34 " pdb=" C6 U8U Y 34 " ideal model delta sigma weight residual 1.506 1.370 0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C1' GCP Z 401 " pdb=" N9 GCP Z 401 " ideal model delta sigma weight residual 1.463 1.561 -0.098 2.00e-02 2.50e+03 2.38e+01 ... (remaining 166775 not shown) Histogram of bond angle deviations from ideal: 94.07 - 105.42: 24173 105.42 - 116.77: 125517 116.77 - 128.12: 91335 128.12 - 139.46: 7994 139.46 - 150.81: 2 Bond angle restraints: 249021 Sorted by residual: angle pdb=" N ARG09 51 " pdb=" CA ARG09 51 " pdb=" C ARG09 51 " ideal model delta sigma weight residual 112.54 124.23 -11.69 1.22e+00 6.72e-01 9.19e+01 angle pdb=" N LYS23 96 " pdb=" CA LYS23 96 " pdb=" C LYS23 96 " ideal model delta sigma weight residual 110.52 96.40 14.12 1.48e+00 4.57e-01 9.11e+01 angle pdb=" N ASN T 69 " pdb=" CA ASN T 69 " pdb=" C ASN T 69 " ideal model delta sigma weight residual 113.41 102.16 11.25 1.22e+00 6.72e-01 8.50e+01 angle pdb=" N LEU03 185 " pdb=" CA LEU03 185 " pdb=" C LEU03 185 " ideal model delta sigma weight residual 112.89 101.97 10.92 1.24e+00 6.50e-01 7.75e+01 angle pdb=" N ARG D 46 " pdb=" CA ARG D 46 " pdb=" C ARG D 46 " ideal model delta sigma weight residual 112.89 102.04 10.85 1.24e+00 6.50e-01 7.65e+01 ... (remaining 249016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 95217 35.98 - 71.96: 10377 71.96 - 107.94: 1166 107.94 - 143.92: 12 143.92 - 179.90: 20 Dihedral angle restraints: 106792 sinusoidal: 88364 harmonic: 18428 Sorted by residual: dihedral pdb=" C5' A A 246 " pdb=" C4' A A 246 " pdb=" C3' A A 246 " pdb=" O3' A A 246 " ideal model delta sinusoidal sigma weight residual 147.00 73.66 73.34 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" O4' C02 12 " pdb=" C1' C02 12 " pdb=" N1 C02 12 " pdb=" C2 C02 12 " ideal model delta sinusoidal sigma weight residual 200.00 31.70 168.30 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' U Y 55 " pdb=" C1' U Y 55 " pdb=" N1 U Y 55 " pdb=" C2 U Y 55 " ideal model delta sinusoidal sigma weight residual 200.00 39.85 160.15 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 106789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 28512 0.137 - 0.274: 3123 0.274 - 0.411: 130 0.411 - 0.547: 8 0.547 - 0.684: 2 Chirality restraints: 31775 Sorted by residual: chirality pdb=" C3' GCP Z 401 " pdb=" C2' GCP Z 401 " pdb=" C4' GCP Z 401 " pdb=" O3' GCP Z 401 " both_signs ideal model delta sigma weight residual False -2.57 -3.25 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" P G Y 1 " pdb=" OP1 G Y 1 " pdb=" OP2 G Y 1 " pdb=" O5' G Y 1 " both_signs ideal model delta sigma weight residual True 2.41 3.01 -0.60 2.00e-01 2.50e+01 9.05e+00 chirality pdb=" C3' A011020 " pdb=" C4' A011020 " pdb=" O3' A011020 " pdb=" C2' A011020 " both_signs ideal model delta sigma weight residual False -2.74 -2.25 -0.49 2.00e-01 2.50e+01 6.07e+00 ... (remaining 31772 not shown) Planarity restraints: 13713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U011818 " -0.097 2.00e-02 2.50e+03 5.25e-02 6.19e+01 pdb=" N1 U011818 " 0.007 2.00e-02 2.50e+03 pdb=" C2 U011818 " 0.020 2.00e-02 2.50e+03 pdb=" O2 U011818 " 0.034 2.00e-02 2.50e+03 pdb=" N3 U011818 " 0.017 2.00e-02 2.50e+03 pdb=" C4 U011818 " 0.016 2.00e-02 2.50e+03 pdb=" O4 U011818 " -0.092 2.00e-02 2.50e+03 pdb=" C5 U011818 " 0.049 2.00e-02 2.50e+03 pdb=" C6 U011818 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G V 18 " 0.107 2.00e-02 2.50e+03 4.39e-02 5.78e+01 pdb=" N9 G V 18 " -0.008 2.00e-02 2.50e+03 pdb=" C8 G V 18 " -0.048 2.00e-02 2.50e+03 pdb=" N7 G V 18 " -0.040 2.00e-02 2.50e+03 pdb=" C5 G V 18 " -0.018 2.00e-02 2.50e+03 pdb=" C6 G V 18 " 0.020 2.00e-02 2.50e+03 pdb=" O6 G V 18 " 0.065 2.00e-02 2.50e+03 pdb=" N1 G V 18 " 0.015 2.00e-02 2.50e+03 pdb=" C2 G V 18 " -0.012 2.00e-02 2.50e+03 pdb=" N2 G V 18 " -0.019 2.00e-02 2.50e+03 pdb=" N3 G V 18 " -0.032 2.00e-02 2.50e+03 pdb=" C4 G V 18 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U Y 29 " -0.091 2.00e-02 2.50e+03 4.95e-02 5.51e+01 pdb=" N1 U Y 29 " 0.004 2.00e-02 2.50e+03 pdb=" C2 U Y 29 " 0.018 2.00e-02 2.50e+03 pdb=" O2 U Y 29 " 0.033 2.00e-02 2.50e+03 pdb=" N3 U Y 29 " 0.017 2.00e-02 2.50e+03 pdb=" C4 U Y 29 " 0.016 2.00e-02 2.50e+03 pdb=" O4 U Y 29 " -0.088 2.00e-02 2.50e+03 pdb=" C5 U Y 29 " 0.047 2.00e-02 2.50e+03 pdb=" C6 U Y 29 " 0.043 2.00e-02 2.50e+03 ... (remaining 13710 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 41966 2.85 - 3.36: 135679 3.36 - 3.87: 321403 3.87 - 4.39: 382554 4.39 - 4.90: 502981 Nonbonded interactions: 1384583 Sorted by model distance: nonbonded pdb=" N GLY20 50 " pdb=" N VAL20 51 " model vdw 2.337 2.560 nonbonded pdb=" O ALA G 144 " pdb=" N ALA G 146 " model vdw 2.338 2.520 nonbonded pdb=" O VAL P 78 " pdb=" O ASN P 79 " model vdw 2.356 3.040 nonbonded pdb=" N GLY H 67 " pdb=" N LYS H 68 " model vdw 2.365 2.560 nonbonded pdb=" N ALA N 21 " pdb=" N LYS N 22 " model vdw 2.370 2.560 ... (remaining 1384578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.69 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 26.590 Check model and map are aligned: 1.660 Set scattering table: 1.020 Process input model: 541.350 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 582.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 166780 Z= 0.430 Angle : 1.031 26.042 249021 Z= 0.680 Chirality : 0.089 0.684 31775 Planarity : 0.008 0.073 13713 Dihedral : 22.349 179.899 94910 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 2.92 % Allowed : 13.85 % Favored : 83.22 % Rotamer: Outliers : 1.31 % Allowed : 5.56 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.08), residues: 6366 helix: -3.42 (0.08), residues: 1843 sheet: -3.25 (0.14), residues: 989 loop : -3.44 (0.09), residues: 3534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.006 TRP04 247 HIS 0.002 0.000 HIS20 82 PHE 0.037 0.005 PHE07 76 TYR 0.052 0.006 TYR R 31 ARG 0.007 0.001 ARG20 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1913 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1844 time to evaluate : 6.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 174 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8265 (mtt180) REVERT: 04 184 GLU cc_start: 0.8616 (tp30) cc_final: 0.8314 (tp30) REVERT: 04 247 TRP cc_start: 0.9297 (m-90) cc_final: 0.8810 (m100) REVERT: 05 42 ASN cc_start: 0.9005 (m110) cc_final: 0.8490 (t0) REVERT: 05 90 PHE cc_start: 0.8061 (m-80) cc_final: 0.7464 (m-10) REVERT: 05 139 SER cc_start: 0.8989 (t) cc_final: 0.8734 (m) REVERT: 06 77 ILE cc_start: 0.8537 (pt) cc_final: 0.8313 (mt) REVERT: 06 153 LEU cc_start: 0.7751 (tp) cc_final: 0.7465 (mt) REVERT: 06 163 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6851 (m-40) REVERT: 07 77 LYS cc_start: 0.9293 (mtmt) cc_final: 0.9002 (tptp) REVERT: 07 82 TYR cc_start: 0.8959 (t80) cc_final: 0.8665 (t80) REVERT: 07 95 MET cc_start: 0.8966 (ptm) cc_final: 0.8424 (ptm) REVERT: 08 55 ASP cc_start: 0.7413 (t70) cc_final: 0.7213 (t0) REVERT: 08 86 LEU cc_start: 0.8632 (mp) cc_final: 0.8367 (tt) REVERT: 08 146 ASP cc_start: 0.9224 (m-30) cc_final: 0.8586 (m-30) REVERT: 08 175 LYS cc_start: 0.4496 (tttt) cc_final: 0.4260 (tptt) REVERT: 09 8 LYS cc_start: 0.9350 (mmmt) cc_final: 0.9053 (tptp) REVERT: 09 12 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8387 (pp) REVERT: 09 30 LEU cc_start: 0.9432 (mt) cc_final: 0.9221 (mt) REVERT: 09 96 THR cc_start: 0.8898 (p) cc_final: 0.8545 (p) REVERT: 09 97 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7302 (mpp-170) REVERT: 09 115 VAL cc_start: 0.8096 (t) cc_final: 0.7089 (t) REVERT: 10 1 MET cc_start: 0.6426 (tpt) cc_final: 0.4403 (ttm) REVERT: 10 35 VAL cc_start: 0.8994 (t) cc_final: 0.8495 (p) REVERT: 10 52 MET cc_start: 0.0854 (ttp) cc_final: -0.0193 (mtt) REVERT: 10 69 PHE cc_start: 0.7485 (t80) cc_final: 0.7237 (t80) REVERT: 10 124 ASP cc_start: 0.6468 (m-30) cc_final: 0.5838 (m-30) REVERT: 11 116 MET cc_start: 0.3886 (mmp) cc_final: 0.3351 (tpp) REVERT: 12 25 LEU cc_start: 0.9318 (tp) cc_final: 0.9091 (tp) REVERT: 12 103 ILE cc_start: 0.9061 (mt) cc_final: 0.8857 (mm) REVERT: 13 78 ARG cc_start: 0.8667 (mtm180) cc_final: 0.8371 (mtm180) REVERT: 14 10 GLU cc_start: 0.8034 (tp30) cc_final: 0.7641 (pp20) REVERT: 15 9 PHE cc_start: 0.8014 (m-80) cc_final: 0.7729 (m-10) REVERT: 15 12 MET cc_start: 0.8069 (ptm) cc_final: 0.7869 (mmm) REVERT: 15 28 PHE cc_start: 0.9216 (m-80) cc_final: 0.8911 (m-80) REVERT: 15 60 GLN cc_start: 0.8342 (pp30) cc_final: 0.7870 (pp30) REVERT: 15 65 ILE cc_start: 0.8880 (mt) cc_final: 0.8637 (tt) REVERT: 15 74 THR cc_start: 0.8705 (p) cc_final: 0.8418 (t) REVERT: 16 18 GLN cc_start: 0.8610 (tt0) cc_final: 0.8157 (tm-30) REVERT: 16 20 MET cc_start: 0.9021 (ppp) cc_final: 0.8206 (ttt) REVERT: 16 43 GLU cc_start: 0.8924 (tp30) cc_final: 0.8551 (mm-30) REVERT: 17 27 VAL cc_start: 0.9122 (t) cc_final: 0.8901 (m) REVERT: 17 60 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8333 (mt-10) REVERT: 17 103 VAL cc_start: 0.9581 (m) cc_final: 0.9342 (p) REVERT: 18 4 ILE cc_start: 0.8961 (mt) cc_final: 0.8700 (mm) REVERT: 18 5 LYS cc_start: 0.8965 (tptt) cc_final: 0.8589 (mptt) REVERT: 18 12 MET cc_start: 0.8409 (ttp) cc_final: 0.8080 (ttm) REVERT: 19 23 TYR cc_start: 0.8582 (m-10) cc_final: 0.8190 (m-10) REVERT: 19 61 ILE cc_start: 0.9586 (mt) cc_final: 0.9144 (tt) REVERT: 19 69 ARG cc_start: 0.8959 (mtt-85) cc_final: 0.8707 (mmt90) REVERT: 19 99 VAL cc_start: 0.9379 (t) cc_final: 0.9136 (m) REVERT: 20 11 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: 20 27 ILE cc_start: 0.8505 (mm) cc_final: 0.7711 (mm) REVERT: 20 82 HIS cc_start: 0.7923 (t-90) cc_final: 0.7552 (t-170) REVERT: 21 52 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8509 (pt0) REVERT: 23 45 GLN cc_start: 0.8844 (tt0) cc_final: 0.8481 (tm-30) REVERT: 23 95 PHE cc_start: 0.9088 (m-80) cc_final: 0.8881 (m-80) REVERT: 24 51 GLN cc_start: 0.9289 (pt0) cc_final: 0.8835 (pt0) REVERT: 25 40 LYS cc_start: 0.8438 (mttt) cc_final: 0.8103 (ptpp) REVERT: 25 64 LYS cc_start: 0.9158 (tppp) cc_final: 0.8772 (tppt) REVERT: 26 37 PHE cc_start: 0.9113 (m-80) cc_final: 0.8575 (m-10) REVERT: 26 49 ARG cc_start: 0.8351 (ttt180) cc_final: 0.8134 (ttp80) REVERT: 26 69 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8754 (mt-10) REVERT: 26 70 LEU cc_start: 0.9279 (mt) cc_final: 0.9073 (mt) REVERT: 27 44 LYS cc_start: 0.9352 (tttp) cc_final: 0.9149 (mttt) REVERT: 27 59 GLU cc_start: 0.9376 (tt0) cc_final: 0.9156 (mt-10) REVERT: 28 20 LYS cc_start: 0.9340 (mtmm) cc_final: 0.9122 (mtmm) REVERT: 30 14 MET cc_start: 0.9216 (mtm) cc_final: 0.8419 (mpp) REVERT: 30 33 SER cc_start: 0.9339 (m) cc_final: 0.8746 (p) REVERT: 30 45 ASP cc_start: 0.8734 (m-30) cc_final: 0.8248 (t0) REVERT: 31 37 LYS cc_start: 0.8289 (mttm) cc_final: 0.8021 (mmtp) REVERT: 33 54 LEU cc_start: 0.9275 (tp) cc_final: 0.8919 (tt) REVERT: 34 2 LYS cc_start: 0.6372 (mmtt) cc_final: 0.5886 (mmtt) REVERT: B 26 MET cc_start: 0.7038 (mtp) cc_final: 0.6759 (ttp) REVERT: B 51 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9126 (mt-10) REVERT: B 93 HIS cc_start: 0.8671 (m170) cc_final: 0.8262 (m-70) REVERT: B 94 ARG cc_start: 0.7728 (mpt180) cc_final: 0.7088 (tpt170) REVERT: B 138 ARG cc_start: 0.8981 (tpt170) cc_final: 0.8684 (tpp-160) REVERT: C 33 ASP cc_start: 0.9091 (t70) cc_final: 0.8786 (t70) REVERT: C 66 THR cc_start: 0.9690 (m) cc_final: 0.9339 (t) REVERT: C 68 HIS cc_start: 0.9066 (m90) cc_final: 0.8780 (m90) REVERT: C 99 GLN cc_start: 0.8856 (tt0) cc_final: 0.8652 (tt0) REVERT: C 141 MET cc_start: 0.9083 (mmm) cc_final: 0.8807 (mmp) REVERT: C 180 ASP cc_start: 0.8834 (t70) cc_final: 0.8594 (p0) REVERT: C 184 ASN cc_start: 0.8150 (t0) cc_final: 0.7623 (t0) REVERT: D 3 TYR cc_start: 0.7740 (t80) cc_final: 0.7284 (t80) REVERT: D 21 LYS cc_start: 0.7900 (tttt) cc_final: 0.7609 (ttmm) REVERT: D 32 LYS cc_start: 0.8669 (mttt) cc_final: 0.8339 (ttpt) REVERT: D 67 LEU cc_start: 0.8656 (mt) cc_final: 0.8340 (mt) REVERT: D 109 THR cc_start: 0.7180 (p) cc_final: 0.6846 (t) REVERT: E 60 GLN cc_start: 0.8855 (pt0) cc_final: 0.8574 (pp30) REVERT: E 75 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6594 (pp) REVERT: E 127 TYR cc_start: 0.8339 (m-80) cc_final: 0.8023 (m-80) REVERT: E 151 MET cc_start: 0.8905 (mmp) cc_final: 0.8703 (mmm) REVERT: F 1 MET cc_start: 0.8758 (mtm) cc_final: 0.8040 (mtm) REVERT: F 25 TYR cc_start: 0.6898 (m-80) cc_final: 0.6263 (m-80) REVERT: F 36 ILE cc_start: 0.8095 (tp) cc_final: 0.7775 (tp) REVERT: F 39 LEU cc_start: 0.8989 (mt) cc_final: 0.8736 (mp) REVERT: F 82 ASP cc_start: 0.8070 (m-30) cc_final: 0.7768 (t0) REVERT: G 8 GLN cc_start: 0.8308 (pt0) cc_final: 0.7775 (pp30) REVERT: G 139 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8453 (m-30) REVERT: H 8 ASP cc_start: 0.9043 (t70) cc_final: 0.8680 (t70) REVERT: H 112 ASP cc_start: 0.8249 (p0) cc_final: 0.7362 (t70) REVERT: H 126 CYS cc_start: 0.8716 (p) cc_final: 0.8501 (t) REVERT: I 58 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8725 (pm20) REVERT: I 99 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8596 (mttt) REVERT: I 106 ASP cc_start: 0.8508 (t70) cc_final: 0.8249 (t0) REVERT: I 117 LEU cc_start: 0.8952 (mp) cc_final: 0.8739 (mp) REVERT: I 122 ARG cc_start: 0.8397 (tpt90) cc_final: 0.7991 (tpt-90) REVERT: J 15 HIS cc_start: 0.8872 (p-80) cc_final: 0.8562 (p90) REVERT: J 27 GLU cc_start: 0.9471 (tp30) cc_final: 0.9212 (tm-30) REVERT: J 28 THR cc_start: 0.8289 (m) cc_final: 0.7890 (t) REVERT: J 63 ASP cc_start: 0.7265 (t0) cc_final: 0.7048 (t0) REVERT: J 66 GLU cc_start: 0.7617 (pt0) cc_final: 0.7173 (pt0) REVERT: J 81 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8645 (mp0) REVERT: K 13 LYS cc_start: 0.8840 (tptp) cc_final: 0.8408 (mtmt) REVERT: K 22 ILE cc_start: 0.7972 (mt) cc_final: 0.7608 (tt) REVERT: K 76 TYR cc_start: 0.8847 (m-80) cc_final: 0.8636 (m-10) REVERT: L 23 LEU cc_start: 0.8862 (tp) cc_final: 0.8632 (tt) REVERT: L 26 CYS cc_start: 0.7576 (p) cc_final: 0.7342 (p) REVERT: L 58 ASN cc_start: 0.8498 (p0) cc_final: 0.7840 (p0) REVERT: L 119 LYS cc_start: 0.9020 (mttp) cc_final: 0.8646 (mmmt) REVERT: M 90 HIS cc_start: 0.8702 (m-70) cc_final: 0.8337 (m90) REVERT: M 102 LYS cc_start: 0.9471 (tttt) cc_final: 0.8752 (tptp) REVERT: O 5 GLU cc_start: 0.8525 (tp30) cc_final: 0.8310 (pp20) REVERT: O 41 HIS cc_start: 0.7950 (t70) cc_final: 0.7260 (t70) REVERT: O 72 LYS cc_start: 0.9019 (tppt) cc_final: 0.8752 (tttt) REVERT: P 17 TYR cc_start: 0.7958 (m-80) cc_final: 0.7706 (m-80) REVERT: Q 41 THR cc_start: 0.8108 (m) cc_final: 0.7768 (m) REVERT: Q 79 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8330 (tm-30) REVERT: R 69 TYR cc_start: 0.6386 (m-80) cc_final: 0.6101 (m-80) REVERT: S 22 VAL cc_start: 0.5959 (t) cc_final: 0.5394 (p) REVERT: S 24 SER cc_start: 0.8679 (t) cc_final: 0.8478 (m) REVERT: S 40 PHE cc_start: 0.8771 (m-80) cc_final: 0.8173 (m-80) REVERT: S 42 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7379 (t0) REVERT: S 65 MET cc_start: 0.8545 (mtm) cc_final: 0.7977 (ptp) REVERT: T 9 ARG cc_start: 0.9298 (mmm160) cc_final: 0.9083 (tpp-160) REVERT: T 56 ILE cc_start: 0.8833 (tp) cc_final: 0.8203 (tp) REVERT: T 68 LYS cc_start: 0.8557 (pttp) cc_final: 0.8352 (tmtt) REVERT: T 83 ASN cc_start: 0.9219 (OUTLIER) cc_final: 0.9001 (p0) REVERT: U 8 ASN cc_start: 0.8520 (m-40) cc_final: 0.8189 (m110) REVERT: U 20 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7005 (mtm-85) REVERT: U 27 VAL cc_start: 0.8215 (m) cc_final: 0.7858 (p) REVERT: U 55 HIS cc_start: 0.8411 (t70) cc_final: 0.8193 (m-70) REVERT: U 57 LYS cc_start: 0.8463 (mmpt) cc_final: 0.8163 (ttpp) REVERT: 03 202 THR cc_start: 0.7256 (m) cc_final: 0.6826 (p) REVERT: Z 79 VAL cc_start: 0.8460 (t) cc_final: 0.8077 (t) REVERT: Z 155 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7801 (tm-30) REVERT: Z 247 ILE cc_start: 0.8143 (mt) cc_final: 0.7819 (mm) REVERT: Z 250 THR cc_start: 0.8330 (p) cc_final: 0.8053 (m) REVERT: Z 351 MET cc_start: 0.8328 (mmm) cc_final: 0.8111 (ttt) outliers start: 69 outliers final: 13 residues processed: 1894 average time/residue: 1.5324 time to fit residues: 4938.0957 Evaluate side-chains 1055 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1034 time to evaluate : 5.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 05 residue 40 LEU Chi-restraints excluded: chain 06 residue 163 ASN Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 11 residue 92 PRO Chi-restraints excluded: chain 20 residue 11 GLN Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain T residue 48 LYS Chi-restraints excluded: chain T residue 83 ASN Chi-restraints excluded: chain U residue 20 ARG Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 114 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 929 optimal weight: 30.0000 chunk 834 optimal weight: 20.0000 chunk 463 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 chunk 562 optimal weight: 10.0000 chunk 445 optimal weight: 5.9990 chunk 862 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 524 optimal weight: 20.0000 chunk 642 optimal weight: 20.0000 chunk 999 optimal weight: 20.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 20 ASN 04 36 ASN 04 85 ASN 04 127 ASN 04 133 ASN 04 225 ASN 04 259 ASN 05 32 ASN ** 05 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 130 GLN 05 134 HIS ** 05 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 150 GLN 06 62 GLN ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 20 ASN 07 22 ASN 07 51 ASN 08 21 GLN 08 29 ASN 08 44 HIS ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 4 ASN 10 88 HIS 11 18 ASN 12 40 HIS 12 58 ASN ** 14 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 54 GLN 15 60 GLN 15 97 GLN 16 9 GLN 16 23 ASN 16 31 HIS 16 62 ASN 17 19 GLN ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 18 11 GLN 18 40 GLN 18 51 ASN ** 18 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 58 GLN 19 80 ASN 21 57 ASN ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 68 ASN 23 73 ASN 24 49 ASN 24 75 GLN 26 16 ASN 27 25 GLN 27 27 ASN 27 31 GLN 27 41 HIS 27 58 ASN ** 28 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 48 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 121 GLN B 176 ASN B 177 ASN C 2 GLN C 24 ASN D 40 HIS D 73 ASN D 119 HIS D 125 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN F 68 GLN F 81 ASN G 27 ASN G 67 ASN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN J 35 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN M 11 HIS N 42 ASN O 27 GLN ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 ASN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN R 53 GLN S 55 GLN T 2 ASN T 12 GLN T 20 ASN ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS 03 203 GLN ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 ASN ** Z 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 166780 Z= 0.297 Angle : 0.789 13.010 249021 Z= 0.406 Chirality : 0.045 0.387 31775 Planarity : 0.007 0.120 13713 Dihedral : 23.068 179.432 82301 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.17 % Favored : 88.30 % Rotamer: Outliers : 5.05 % Allowed : 16.35 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.09), residues: 6366 helix: -1.78 (0.10), residues: 1952 sheet: -2.77 (0.15), residues: 940 loop : -2.90 (0.09), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 17 HIS 0.010 0.002 HIS03 67 PHE 0.037 0.003 PHE B 49 TYR 0.028 0.002 TYR29 9 ARG 0.016 0.001 ARG08 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1389 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1122 time to evaluate : 6.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 131 MET cc_start: 0.8517 (mpp) cc_final: 0.8305 (mpp) REVERT: 04 174 ARG cc_start: 0.8709 (ttp80) cc_final: 0.8507 (ttm170) REVERT: 04 247 TRP cc_start: 0.9315 (m-90) cc_final: 0.8872 (m100) REVERT: 05 42 ASN cc_start: 0.9011 (m110) cc_final: 0.8167 (t0) REVERT: 05 90 PHE cc_start: 0.8056 (m-80) cc_final: 0.7594 (m-10) REVERT: 06 153 LEU cc_start: 0.7647 (tp) cc_final: 0.7308 (mt) REVERT: 06 163 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7553 (m-40) REVERT: 07 9 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.6976 (p0) REVERT: 07 80 GLN cc_start: 0.8464 (tp40) cc_final: 0.8245 (tp-100) REVERT: 07 82 TYR cc_start: 0.9065 (t80) cc_final: 0.8859 (t80) REVERT: 07 95 MET cc_start: 0.8952 (ptm) cc_final: 0.8391 (ptm) REVERT: 07 146 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.6418 (m-30) REVERT: 08 55 ASP cc_start: 0.7404 (t70) cc_final: 0.7179 (t0) REVERT: 09 4 ILE cc_start: 0.8900 (pt) cc_final: 0.8598 (pt) REVERT: 09 8 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8729 (tptp) REVERT: 09 12 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8434 (pp) REVERT: 09 97 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7468 (mmm-85) REVERT: 09 112 LYS cc_start: 0.6820 (mtmt) cc_final: 0.6559 (mtmt) REVERT: 09 149 GLU cc_start: 0.6716 (tt0) cc_final: 0.6415 (tt0) REVERT: 10 1 MET cc_start: 0.6585 (tpt) cc_final: 0.6192 (tpp) REVERT: 10 46 ARG cc_start: 0.8436 (tpp-160) cc_final: 0.7708 (mmp-170) REVERT: 10 52 MET cc_start: 0.0957 (ttp) cc_final: -0.0123 (mtt) REVERT: 10 53 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7295 (mmp-170) REVERT: 10 69 PHE cc_start: 0.7412 (t80) cc_final: 0.7178 (t80) REVERT: 10 86 MET cc_start: -0.1369 (mmt) cc_final: -0.1805 (mmt) REVERT: 11 59 THR cc_start: 0.7190 (m) cc_final: 0.6965 (m) REVERT: 11 116 MET cc_start: 0.4028 (mmp) cc_final: 0.3706 (tpt) REVERT: 11 135 MET cc_start: 0.4843 (tpp) cc_final: 0.4428 (tpp) REVERT: 13 13 ASN cc_start: 0.8809 (p0) cc_final: 0.8596 (p0) REVERT: 13 106 GLU cc_start: 0.7597 (mp0) cc_final: 0.6958 (mp0) REVERT: 15 60 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8057 (pp30) REVERT: 15 65 ILE cc_start: 0.8907 (mt) cc_final: 0.8706 (tt) REVERT: 16 18 GLN cc_start: 0.9005 (tt0) cc_final: 0.8254 (tm-30) REVERT: 16 54 LEU cc_start: 0.9390 (tp) cc_final: 0.9125 (tt) REVERT: 18 12 MET cc_start: 0.8644 (ttp) cc_final: 0.8319 (ttm) REVERT: 18 51 ASN cc_start: 0.7107 (t0) cc_final: 0.6838 (t0) REVERT: 20 16 GLU cc_start: 0.8826 (tt0) cc_final: 0.8305 (tp30) REVERT: 20 48 LYS cc_start: 0.8213 (pttm) cc_final: 0.7916 (pttt) REVERT: 20 82 HIS cc_start: 0.8406 (t-90) cc_final: 0.7899 (t-170) REVERT: 21 52 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8446 (pt0) REVERT: 22 1 MET cc_start: 0.4551 (ptp) cc_final: 0.4156 (mtt) REVERT: 22 42 GLU cc_start: 0.8224 (mp0) cc_final: 0.8015 (mp0) REVERT: 22 79 ASP cc_start: 0.8917 (m-30) cc_final: 0.8713 (m-30) REVERT: 23 45 GLN cc_start: 0.8881 (tt0) cc_final: 0.8522 (tm-30) REVERT: 24 51 GLN cc_start: 0.9119 (pt0) cc_final: 0.8874 (pt0) REVERT: 25 40 LYS cc_start: 0.8468 (mttt) cc_final: 0.7786 (pttt) REVERT: 25 64 LYS cc_start: 0.9126 (tppp) cc_final: 0.8817 (tppt) REVERT: 26 69 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8743 (mt-10) REVERT: 27 59 GLU cc_start: 0.9417 (tt0) cc_final: 0.9093 (mt-10) REVERT: 28 18 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8318 (mmtt) REVERT: 28 20 LYS cc_start: 0.9359 (mtmm) cc_final: 0.9116 (mtmt) REVERT: 30 27 LEU cc_start: 0.9003 (mp) cc_final: 0.8502 (mt) REVERT: 30 33 SER cc_start: 0.9299 (m) cc_final: 0.9055 (p) REVERT: 30 45 ASP cc_start: 0.8910 (m-30) cc_final: 0.8311 (t70) REVERT: 31 29 LYS cc_start: 0.7775 (mmmt) cc_final: 0.7328 (mmmm) REVERT: 32 8 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8178 (p) REVERT: 32 22 MET cc_start: 0.8491 (mmm) cc_final: 0.8206 (tpp) REVERT: 34 2 LYS cc_start: 0.6587 (mmtt) cc_final: 0.6132 (mmtt) REVERT: 34 36 ARG cc_start: 0.8436 (tmm-80) cc_final: 0.8081 (ptm-80) REVERT: B 26 MET cc_start: 0.7184 (mtp) cc_final: 0.6727 (ttp) REVERT: B 36 LYS cc_start: 0.7222 (mttp) cc_final: 0.6533 (tptt) REVERT: B 49 PHE cc_start: 0.8970 (p90) cc_final: 0.8532 (p90) REVERT: B 55 GLU cc_start: 0.9255 (mm-30) cc_final: 0.9033 (mp0) REVERT: B 93 HIS cc_start: 0.8608 (m170) cc_final: 0.7977 (m-70) REVERT: B 94 ARG cc_start: 0.7922 (mpt180) cc_final: 0.6930 (tpm170) REVERT: B 138 ARG cc_start: 0.9093 (tpt170) cc_final: 0.8739 (tpp-160) REVERT: C 114 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7720 (mp) REVERT: C 128 MET cc_start: 0.8309 (tpt) cc_final: 0.8069 (tpt) REVERT: C 146 LYS cc_start: 0.7981 (mmtp) cc_final: 0.7759 (mttp) REVERT: C 167 TYR cc_start: 0.8001 (m-80) cc_final: 0.7789 (m-80) REVERT: C 180 ASP cc_start: 0.8971 (t70) cc_final: 0.8594 (p0) REVERT: C 182 ASP cc_start: 0.8280 (t0) cc_final: 0.7940 (t0) REVERT: D 3 TYR cc_start: 0.7860 (t80) cc_final: 0.7335 (t80) REVERT: D 32 LYS cc_start: 0.8789 (mttt) cc_final: 0.8307 (ttpt) REVERT: D 53 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7779 (mm110) REVERT: D 87 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.9008 (mp0) REVERT: D 165 GLU cc_start: 0.8046 (pm20) cc_final: 0.7838 (pm20) REVERT: E 12 GLU cc_start: 0.6766 (pt0) cc_final: 0.6407 (pm20) REVERT: E 60 GLN cc_start: 0.8889 (pt0) cc_final: 0.8613 (tm-30) REVERT: E 127 TYR cc_start: 0.8288 (m-80) cc_final: 0.7890 (m-80) REVERT: F 11 HIS cc_start: 0.9086 (t70) cc_final: 0.8788 (t-90) REVERT: F 14 GLN cc_start: 0.8911 (tt0) cc_final: 0.8446 (tm-30) REVERT: F 65 GLU cc_start: 0.8513 (tt0) cc_final: 0.8200 (tm-30) REVERT: F 82 ASP cc_start: 0.8207 (m-30) cc_final: 0.7717 (t0) REVERT: F 91 ARG cc_start: 0.8793 (mtt180) cc_final: 0.8428 (tpm170) REVERT: F 98 GLU cc_start: 0.8314 (mp0) cc_final: 0.7896 (mp0) REVERT: G 8 GLN cc_start: 0.8239 (pt0) cc_final: 0.7676 (pp30) REVERT: H 59 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: H 89 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8444 (p0) REVERT: I 87 MET cc_start: 0.8906 (mmm) cc_final: 0.8607 (mmm) REVERT: I 106 ASP cc_start: 0.8555 (t70) cc_final: 0.8219 (t0) REVERT: J 15 HIS cc_start: 0.8704 (p-80) cc_final: 0.8492 (p90) REVERT: J 28 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7364 (t) REVERT: J 65 TYR cc_start: 0.6579 (m-80) cc_final: 0.5851 (m-80) REVERT: J 81 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8443 (mp0) REVERT: J 100 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6763 (mp) REVERT: K 13 LYS cc_start: 0.8746 (tptp) cc_final: 0.8402 (mtmt) REVERT: L 56 LEU cc_start: 0.7989 (tp) cc_final: 0.7765 (tp) REVERT: M 90 HIS cc_start: 0.8756 (m-70) cc_final: 0.8309 (m90) REVERT: M 92 ARG cc_start: 0.9207 (mtp85) cc_final: 0.8895 (ptt180) REVERT: M 101 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8842 (p) REVERT: M 102 LYS cc_start: 0.9447 (tttt) cc_final: 0.8867 (tttm) REVERT: O 41 HIS cc_start: 0.7654 (t70) cc_final: 0.7016 (t-90) REVERT: O 45 HIS cc_start: 0.8662 (m170) cc_final: 0.8372 (m90) REVERT: O 47 LYS cc_start: 0.8004 (pttt) cc_final: 0.7783 (pttm) REVERT: O 72 LYS cc_start: 0.9018 (tppt) cc_final: 0.8765 (tttt) REVERT: R 49 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7716 (ttmm) REVERT: R 69 TYR cc_start: 0.6842 (m-80) cc_final: 0.6321 (m-80) REVERT: S 40 PHE cc_start: 0.8768 (m-80) cc_final: 0.8529 (m-80) REVERT: S 42 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7119 (t0) REVERT: S 65 MET cc_start: 0.8506 (mtm) cc_final: 0.8068 (ptp) REVERT: T 56 ILE cc_start: 0.8896 (tp) cc_final: 0.8088 (tp) REVERT: T 58 ASP cc_start: 0.8530 (t0) cc_final: 0.8176 (p0) REVERT: U 54 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6618 (mmm160) REVERT: U 55 HIS cc_start: 0.8551 (t70) cc_final: 0.8304 (m90) REVERT: U 57 LYS cc_start: 0.8482 (mmpt) cc_final: 0.8034 (tmtt) REVERT: 03 53 ARG cc_start: 0.6790 (mpt180) cc_final: 0.6436 (mmt90) REVERT: 03 218 MET cc_start: 0.6394 (mtp) cc_final: 0.6110 (mtm) REVERT: Z 123 ARG cc_start: 0.8558 (tpm170) cc_final: 0.7436 (tmt170) REVERT: Z 155 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7818 (tm-30) REVERT: Z 159 GLN cc_start: 0.7000 (tt0) cc_final: 0.6580 (tt0) outliers start: 267 outliers final: 137 residues processed: 1282 average time/residue: 1.3971 time to fit residues: 3099.0024 Evaluate side-chains 1037 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 884 time to evaluate : 6.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 87 SER Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 40 LEU Chi-restraints excluded: chain 05 residue 51 THR Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 203 VAL Chi-restraints excluded: chain 06 residue 113 VAL Chi-restraints excluded: chain 06 residue 126 VAL Chi-restraints excluded: chain 06 residue 144 GLU Chi-restraints excluded: chain 06 residue 163 ASN Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 10 residue 53 ARG Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 27 LEU Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 12 residue 19 ASP Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 60 GLN Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 16 residue 120 GLU Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 19 residue 39 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 25 LEU Chi-restraints excluded: chain 20 residue 41 ILE Chi-restraints excluded: chain 20 residue 49 ILE Chi-restraints excluded: chain 20 residue 55 ASP Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 71 VAL Chi-restraints excluded: chain 21 residue 107 VAL Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 93 LEU Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 45 ASP Chi-restraints excluded: chain 26 residue 10 ARG Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 29 residue 4 ASP Chi-restraints excluded: chain 30 residue 21 LEU Chi-restraints excluded: chain 30 residue 36 LYS Chi-restraints excluded: chain 31 residue 25 ASN Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 8 SER Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 84 ARG Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 10 PRO Chi-restraints excluded: chain U residue 54 ARG Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 69 THR Chi-restraints excluded: chain 03 residue 192 LEU Chi-restraints excluded: chain Z residue 13 ASN Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 320 THR Chi-restraints excluded: chain Z residue 329 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 555 optimal weight: 5.9990 chunk 310 optimal weight: 20.0000 chunk 832 optimal weight: 30.0000 chunk 680 optimal weight: 20.0000 chunk 275 optimal weight: 40.0000 chunk 1001 optimal weight: 20.0000 chunk 1082 optimal weight: 0.5980 chunk 892 optimal weight: 30.0000 chunk 993 optimal weight: 20.0000 chunk 341 optimal weight: 20.0000 chunk 803 optimal weight: 30.0000 overall best weight: 13.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 04 238 ASN ** 06 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 07 20 ASN ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 11 ASN 11 30 GLN ** 11 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 23 ASN 16 73 ASN ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 17 116 GLN 18 40 GLN ** 18 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 86 GLN ** 20 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 25 8 ASN 26 16 ASN 28 48 ASN B 14 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 125 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 ASN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS ** 03 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 159 GLN ** Z 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 166780 Z= 0.376 Angle : 0.815 15.468 249021 Z= 0.418 Chirality : 0.043 0.367 31775 Planarity : 0.007 0.072 13713 Dihedral : 23.662 179.711 82270 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 32.45 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.92 % Favored : 85.66 % Rotamer: Outliers : 6.93 % Allowed : 17.79 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.09), residues: 6366 helix: -1.45 (0.10), residues: 1953 sheet: -2.55 (0.15), residues: 975 loop : -2.81 (0.10), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 17 HIS 0.013 0.002 HIS F 55 PHE 0.028 0.003 PHE R 12 TYR 0.046 0.003 TYR B 212 ARG 0.016 0.001 ARG R 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 908 time to evaluate : 6.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 131 MET cc_start: 0.8649 (mpp) cc_final: 0.8343 (mpp) REVERT: 05 42 ASN cc_start: 0.8985 (m110) cc_final: 0.8198 (t0) REVERT: 05 90 PHE cc_start: 0.8139 (m-80) cc_final: 0.7727 (m-10) REVERT: 06 62 GLN cc_start: 0.7609 (tt0) cc_final: 0.7267 (tt0) REVERT: 06 153 LEU cc_start: 0.7498 (tp) cc_final: 0.6959 (mt) REVERT: 06 163 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7442 (m-40) REVERT: 07 82 TYR cc_start: 0.9019 (t80) cc_final: 0.8655 (t80) REVERT: 07 89 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7933 (p) REVERT: 07 95 MET cc_start: 0.8736 (ptm) cc_final: 0.8519 (ptm) REVERT: 08 55 ASP cc_start: 0.7168 (t70) cc_final: 0.6946 (t0) REVERT: 09 8 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8691 (tptp) REVERT: 09 12 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8406 (pp) REVERT: 09 97 ARG cc_start: 0.8451 (mtt180) cc_final: 0.7572 (mmm-85) REVERT: 09 112 LYS cc_start: 0.6476 (mtmt) cc_final: 0.6273 (mtmt) REVERT: 10 1 MET cc_start: 0.6706 (tpt) cc_final: 0.6496 (tpp) REVERT: 10 51 TYR cc_start: 0.3782 (OUTLIER) cc_final: 0.3574 (p90) REVERT: 10 52 MET cc_start: 0.0892 (ttp) cc_final: -0.0019 (mtt) REVERT: 10 86 MET cc_start: -0.1562 (mmt) cc_final: -0.2407 (mmt) REVERT: 10 122 GLN cc_start: 0.8243 (pm20) cc_final: 0.7906 (pp30) REVERT: 11 59 THR cc_start: 0.7014 (m) cc_final: 0.6772 (m) REVERT: 11 116 MET cc_start: 0.4044 (mmp) cc_final: 0.3557 (tpt) REVERT: 11 135 MET cc_start: 0.4567 (tpp) cc_final: 0.3915 (tpp) REVERT: 13 7 MET cc_start: 0.8896 (mmm) cc_final: 0.8664 (mmt) REVERT: 13 93 GLN cc_start: 0.8162 (mp10) cc_final: 0.7836 (mp10) REVERT: 14 55 MET cc_start: 0.8612 (tpt) cc_final: 0.8376 (tpt) REVERT: 14 58 TYR cc_start: 0.8942 (p90) cc_final: 0.8730 (p90) REVERT: 14 115 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6311 (tm-30) REVERT: 15 60 GLN cc_start: 0.8599 (pp30) cc_final: 0.8310 (pp30) REVERT: 16 18 GLN cc_start: 0.9117 (tt0) cc_final: 0.8309 (tm-30) REVERT: 16 20 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.7527 (ppp) REVERT: 16 24 MET cc_start: 0.8290 (ptm) cc_final: 0.7871 (ptm) REVERT: 16 34 ILE cc_start: 0.8702 (pp) cc_final: 0.8501 (pp) REVERT: 16 75 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9183 (mm) REVERT: 17 94 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8288 (ttp-170) REVERT: 18 12 MET cc_start: 0.8714 (ttp) cc_final: 0.8486 (ttm) REVERT: 18 51 ASN cc_start: 0.7135 (t0) cc_final: 0.6842 (t0) REVERT: 20 82 HIS cc_start: 0.8459 (t-90) cc_final: 0.8066 (t-170) REVERT: 20 94 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8956 (m) REVERT: 21 18 ARG cc_start: 0.8596 (mtt180) cc_final: 0.8371 (mtt180) REVERT: 21 52 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8391 (pt0) REVERT: 22 1 MET cc_start: 0.5046 (ptp) cc_final: 0.4456 (mtt) REVERT: 22 42 GLU cc_start: 0.8617 (mp0) cc_final: 0.8368 (mp0) REVERT: 23 17 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.7674 (t0) REVERT: 23 45 GLN cc_start: 0.9031 (tt0) cc_final: 0.8622 (pp30) REVERT: 24 29 ILE cc_start: 0.8297 (tt) cc_final: 0.8094 (pt) REVERT: 25 40 LYS cc_start: 0.8614 (mttt) cc_final: 0.7763 (mttp) REVERT: 25 64 LYS cc_start: 0.9095 (tppp) cc_final: 0.8867 (tppt) REVERT: 26 37 PHE cc_start: 0.9185 (m-80) cc_final: 0.8766 (m-10) REVERT: 26 69 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8692 (mt-10) REVERT: 27 59 GLU cc_start: 0.9415 (tt0) cc_final: 0.9126 (mt-10) REVERT: 28 18 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8282 (mmtt) REVERT: 28 20 LYS cc_start: 0.9328 (mtmm) cc_final: 0.9118 (mtmm) REVERT: 28 53 MET cc_start: 0.8610 (ptt) cc_final: 0.7903 (mtp) REVERT: 29 1 MET cc_start: 0.7612 (mtt) cc_final: 0.7315 (ppp) REVERT: 30 27 LEU cc_start: 0.9030 (mp) cc_final: 0.8642 (mt) REVERT: 30 45 ASP cc_start: 0.8968 (m-30) cc_final: 0.8245 (t0) REVERT: 31 29 LYS cc_start: 0.7754 (mmmt) cc_final: 0.7461 (mmtp) REVERT: 31 32 LYS cc_start: 0.6601 (tttt) cc_final: 0.6384 (mptt) REVERT: 34 2 LYS cc_start: 0.7089 (mmtt) cc_final: 0.6643 (mmtt) REVERT: B 19 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7450 (t) REVERT: B 25 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8762 (mtpp) REVERT: B 26 MET cc_start: 0.7210 (mtp) cc_final: 0.6519 (ttp) REVERT: B 36 LYS cc_start: 0.7175 (mttp) cc_final: 0.6363 (tptt) REVERT: B 37 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7786 (t) REVERT: B 93 HIS cc_start: 0.8603 (m170) cc_final: 0.8032 (m-70) REVERT: B 94 ARG cc_start: 0.7880 (mpt180) cc_final: 0.7059 (tpt170) REVERT: B 119 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6446 (pp30) REVERT: B 130 LYS cc_start: 0.8308 (tmmt) cc_final: 0.8008 (tptp) REVERT: C 128 MET cc_start: 0.8251 (tpt) cc_final: 0.7992 (tpt) REVERT: C 180 ASP cc_start: 0.9000 (t70) cc_final: 0.8588 (p0) REVERT: C 182 ASP cc_start: 0.8506 (t0) cc_final: 0.8172 (t0) REVERT: D 3 TYR cc_start: 0.7882 (t80) cc_final: 0.7465 (t80) REVERT: D 53 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7925 (mm110) REVERT: E 12 GLU cc_start: 0.6682 (pt0) cc_final: 0.6280 (pm20) REVERT: E 60 GLN cc_start: 0.8975 (pt0) cc_final: 0.8614 (tm-30) REVERT: E 127 TYR cc_start: 0.8446 (m-80) cc_final: 0.8194 (m-80) REVERT: F 1 MET cc_start: 0.8015 (mtm) cc_final: 0.7264 (ttm) REVERT: F 11 HIS cc_start: 0.9223 (t-90) cc_final: 0.8560 (t-90) REVERT: F 65 GLU cc_start: 0.8289 (tt0) cc_final: 0.7789 (tm-30) REVERT: F 75 GLU cc_start: 0.9388 (pt0) cc_final: 0.9167 (pp20) REVERT: G 8 GLN cc_start: 0.8335 (pt0) cc_final: 0.7713 (pp30) REVERT: H 12 ARG cc_start: 0.8727 (mpt-90) cc_final: 0.8511 (mpt-90) REVERT: H 26 MET cc_start: 0.7901 (ppp) cc_final: 0.7541 (ppp) REVERT: I 87 MET cc_start: 0.8976 (mmm) cc_final: 0.8754 (mmm) REVERT: I 89 TYR cc_start: 0.7536 (m-80) cc_final: 0.7245 (m-80) REVERT: I 99 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8567 (mttm) REVERT: I 106 ASP cc_start: 0.8442 (t70) cc_final: 0.8161 (t0) REVERT: I 122 ARG cc_start: 0.8246 (tpt90) cc_final: 0.7517 (mmm160) REVERT: J 15 HIS cc_start: 0.8669 (p-80) cc_final: 0.8439 (p90) REVERT: J 65 TYR cc_start: 0.6760 (m-80) cc_final: 0.6452 (m-80) REVERT: J 81 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8333 (mp0) REVERT: K 13 LYS cc_start: 0.8897 (tptp) cc_final: 0.8572 (mtmt) REVERT: L 6 LEU cc_start: 0.9604 (mt) cc_final: 0.9348 (mp) REVERT: M 71 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9101 (mm-30) REVERT: M 90 HIS cc_start: 0.8984 (m-70) cc_final: 0.8518 (m170) REVERT: M 92 ARG cc_start: 0.9191 (mtp85) cc_final: 0.8669 (mmt-90) REVERT: M 101 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8805 (p) REVERT: M 102 LYS cc_start: 0.9405 (tttt) cc_final: 0.8715 (tttm) REVERT: O 41 HIS cc_start: 0.7638 (t70) cc_final: 0.6950 (t70) REVERT: O 47 LYS cc_start: 0.8024 (pttt) cc_final: 0.7779 (pttm) REVERT: Q 68 LYS cc_start: 0.8541 (mtpt) cc_final: 0.8202 (mtpt) REVERT: R 69 TYR cc_start: 0.6861 (m-80) cc_final: 0.6240 (m-80) REVERT: S 65 MET cc_start: 0.8625 (mtm) cc_final: 0.8058 (ptm) REVERT: T 27 MET cc_start: 0.9411 (mmm) cc_final: 0.8913 (mmm) REVERT: T 56 ILE cc_start: 0.8549 (tp) cc_final: 0.8260 (tp) REVERT: T 58 ASP cc_start: 0.8648 (t0) cc_final: 0.8381 (p0) REVERT: U 20 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6333 (mtm-85) REVERT: U 24 LYS cc_start: 0.6784 (tttp) cc_final: 0.6315 (tttm) REVERT: U 57 LYS cc_start: 0.8434 (mmpt) cc_final: 0.7801 (tmtt) REVERT: 03 53 ARG cc_start: 0.6989 (mpt180) cc_final: 0.6583 (mmt180) REVERT: Z 155 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7444 (tm-30) REVERT: Z 159 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6446 (tt0) outliers start: 366 outliers final: 236 residues processed: 1161 average time/residue: 1.3306 time to fit residues: 2684.0642 Evaluate side-chains 1050 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 798 time to evaluate : 6.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 53 ILE Chi-restraints excluded: chain 04 residue 87 SER Chi-restraints excluded: chain 04 residue 132 ARG Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 04 residue 238 ASN Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 40 LEU Chi-restraints excluded: chain 05 residue 51 THR Chi-restraints excluded: chain 05 residue 100 LEU Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 203 VAL Chi-restraints excluded: chain 05 residue 204 LYS Chi-restraints excluded: chain 06 residue 126 VAL Chi-restraints excluded: chain 06 residue 163 ASN Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 90 LEU Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 106 LEU Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 62 LEU Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 10 residue 50 VAL Chi-restraints excluded: chain 10 residue 51 TYR Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 27 LEU Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 19 ASP Chi-restraints excluded: chain 12 residue 60 ASP Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 103 ILE Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 109 SER Chi-restraints excluded: chain 13 residue 118 LEU Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 27 SER Chi-restraints excluded: chain 16 residue 29 VAL Chi-restraints excluded: chain 16 residue 73 ASN Chi-restraints excluded: chain 16 residue 75 ILE Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 16 residue 120 GLU Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 94 ARG Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 19 residue 39 ILE Chi-restraints excluded: chain 19 residue 75 TYR Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 13 ARG Chi-restraints excluded: chain 20 residue 41 ILE Chi-restraints excluded: chain 20 residue 94 THR Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 71 VAL Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 40 LEU Chi-restraints excluded: chain 23 residue 58 VAL Chi-restraints excluded: chain 23 residue 65 GLN Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 45 ASP Chi-restraints excluded: chain 25 residue 32 ILE Chi-restraints excluded: chain 25 residue 76 ILE Chi-restraints excluded: chain 26 residue 10 ARG Chi-restraints excluded: chain 26 residue 16 ASN Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 29 residue 4 ASP Chi-restraints excluded: chain 29 residue 35 ASP Chi-restraints excluded: chain 29 residue 47 LYS Chi-restraints excluded: chain 29 residue 66 ILE Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 21 LEU Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 8 SER Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 51 GLN Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 84 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 71 SER Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 10 PRO Chi-restraints excluded: chain U residue 11 PHE Chi-restraints excluded: chain U residue 20 ARG Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 48 LEU Chi-restraints excluded: chain 03 residue 69 THR Chi-restraints excluded: chain 03 residue 192 LEU Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 13 ASN Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 159 GLN Chi-restraints excluded: chain Z residue 211 LEU Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Z residue 320 THR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 989 optimal weight: 20.0000 chunk 753 optimal weight: 20.0000 chunk 519 optimal weight: 20.0000 chunk 110 optimal weight: 30.0000 chunk 478 optimal weight: 10.0000 chunk 672 optimal weight: 20.0000 chunk 1005 optimal weight: 20.0000 chunk 1064 optimal weight: 6.9990 chunk 525 optimal weight: 20.0000 chunk 952 optimal weight: 30.0000 chunk 286 optimal weight: 1.9990 overall best weight: 11.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 61 GLN ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 48 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 77 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 HIS ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS ** 03 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 166780 Z= 0.330 Angle : 0.747 18.066 249021 Z= 0.385 Chirality : 0.041 0.365 31775 Planarity : 0.006 0.061 13713 Dihedral : 23.861 179.579 82267 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 30.43 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.61 % Favored : 86.96 % Rotamer: Outliers : 7.04 % Allowed : 19.77 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.10), residues: 6366 helix: -1.14 (0.11), residues: 1934 sheet: -2.40 (0.15), residues: 1000 loop : -2.71 (0.10), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 17 HIS 0.010 0.002 HIS D 197 PHE 0.027 0.003 PHE B 49 TYR 0.027 0.002 TYR O 77 ARG 0.009 0.001 ARG D 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 865 time to evaluate : 6.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 131 MET cc_start: 0.8590 (mpp) cc_final: 0.8344 (mpp) REVERT: 05 42 ASN cc_start: 0.9000 (m110) cc_final: 0.8238 (t0) REVERT: 05 90 PHE cc_start: 0.8120 (m-80) cc_final: 0.7712 (m-10) REVERT: 06 100 MET cc_start: 0.8913 (mtt) cc_final: 0.8284 (mmt) REVERT: 06 153 LEU cc_start: 0.7483 (tp) cc_final: 0.6936 (mt) REVERT: 06 188 MET cc_start: 0.9189 (mmm) cc_final: 0.8833 (mmm) REVERT: 07 25 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8623 (mtp) REVERT: 07 80 GLN cc_start: 0.8371 (tp40) cc_final: 0.8081 (tp-100) REVERT: 07 82 TYR cc_start: 0.8889 (t80) cc_final: 0.8516 (t80) REVERT: 07 89 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7792 (p) REVERT: 09 8 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8237 (tptp) REVERT: 09 12 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8334 (pp) REVERT: 09 70 GLU cc_start: 0.4432 (OUTLIER) cc_final: 0.4121 (tp30) REVERT: 10 52 MET cc_start: 0.1010 (ttp) cc_final: 0.0057 (mtt) REVERT: 10 86 MET cc_start: -0.1458 (mmt) cc_final: -0.2265 (mmt) REVERT: 10 122 GLN cc_start: 0.8037 (pm20) cc_final: 0.7584 (tm-30) REVERT: 11 59 THR cc_start: 0.7068 (m) cc_final: 0.6834 (m) REVERT: 11 116 MET cc_start: 0.3406 (mmp) cc_final: 0.2759 (tpp) REVERT: 11 135 MET cc_start: 0.4744 (tpp) cc_final: 0.4020 (tpp) REVERT: 12 31 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8511 (tm-30) REVERT: 13 49 ARG cc_start: 0.8590 (mmp-170) cc_final: 0.8314 (mmp-170) REVERT: 13 121 GLU cc_start: 0.8353 (pt0) cc_final: 0.8057 (pt0) REVERT: 14 115 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6511 (tm-30) REVERT: 14 144 GLU cc_start: 0.6505 (pt0) cc_final: 0.6253 (mm-30) REVERT: 15 60 GLN cc_start: 0.8521 (pp30) cc_final: 0.7933 (pp30) REVERT: 16 18 GLN cc_start: 0.9070 (tt0) cc_final: 0.8241 (tm-30) REVERT: 16 75 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9168 (mm) REVERT: 17 56 LYS cc_start: 0.9275 (pptt) cc_final: 0.8827 (pptt) REVERT: 17 85 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8997 (tttt) REVERT: 17 94 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8204 (ttp-170) REVERT: 18 12 MET cc_start: 0.8695 (ttp) cc_final: 0.8468 (ttm) REVERT: 18 51 ASN cc_start: 0.7081 (t0) cc_final: 0.6780 (t0) REVERT: 20 82 HIS cc_start: 0.8474 (t-90) cc_final: 0.8025 (t-170) REVERT: 20 94 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8928 (m) REVERT: 21 31 GLN cc_start: 0.9230 (mt0) cc_final: 0.8971 (pp30) REVERT: 21 52 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8395 (pt0) REVERT: 22 1 MET cc_start: 0.5151 (ptp) cc_final: 0.4770 (mtt) REVERT: 22 42 GLU cc_start: 0.8660 (mp0) cc_final: 0.8439 (mp0) REVERT: 23 17 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.7795 (t0) REVERT: 23 18 LYS cc_start: 0.9565 (tmmt) cc_final: 0.9317 (mtpt) REVERT: 23 45 GLN cc_start: 0.9046 (tt0) cc_final: 0.8662 (pp30) REVERT: 24 12 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8550 (pp30) REVERT: 24 29 ILE cc_start: 0.8292 (tt) cc_final: 0.8041 (pt) REVERT: 24 45 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8426 (t0) REVERT: 25 40 LYS cc_start: 0.8657 (mttt) cc_final: 0.7793 (mttp) REVERT: 25 64 LYS cc_start: 0.9054 (tppp) cc_final: 0.8834 (tppt) REVERT: 26 37 PHE cc_start: 0.9171 (m-80) cc_final: 0.8764 (m-10) REVERT: 26 69 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8662 (mt-10) REVERT: 27 59 GLU cc_start: 0.9416 (tt0) cc_final: 0.9123 (mt-10) REVERT: 28 18 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8280 (mmtt) REVERT: 28 20 LYS cc_start: 0.9325 (mtmm) cc_final: 0.9114 (mtmm) REVERT: 28 53 MET cc_start: 0.8688 (ptt) cc_final: 0.8450 (ptm) REVERT: 30 14 MET cc_start: 0.8997 (mtp) cc_final: 0.8682 (ptp) REVERT: 30 27 LEU cc_start: 0.9019 (mp) cc_final: 0.8667 (mt) REVERT: 30 45 ASP cc_start: 0.9066 (m-30) cc_final: 0.8239 (t70) REVERT: 34 2 LYS cc_start: 0.7021 (mmtt) cc_final: 0.6590 (mmtt) REVERT: B 19 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7436 (t) REVERT: B 26 MET cc_start: 0.7144 (mtp) cc_final: 0.6428 (ttp) REVERT: B 36 LYS cc_start: 0.7262 (mttp) cc_final: 0.6395 (tptt) REVERT: B 93 HIS cc_start: 0.8561 (m170) cc_final: 0.7982 (m-70) REVERT: B 94 ARG cc_start: 0.7831 (mpt180) cc_final: 0.7005 (tpt170) REVERT: C 114 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7969 (mp) REVERT: C 128 MET cc_start: 0.8276 (tpt) cc_final: 0.8062 (tpt) REVERT: C 180 ASP cc_start: 0.9001 (t70) cc_final: 0.8555 (p0) REVERT: C 182 ASP cc_start: 0.8576 (t0) cc_final: 0.8254 (t0) REVERT: D 3 TYR cc_start: 0.7947 (t80) cc_final: 0.7467 (t80) REVERT: D 46 ARG cc_start: 0.6986 (tpm170) cc_final: 0.6313 (tpm170) REVERT: D 135 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8126 (tm-30) REVERT: E 12 GLU cc_start: 0.6501 (pt0) cc_final: 0.6230 (pm20) REVERT: E 60 GLN cc_start: 0.9011 (pt0) cc_final: 0.8736 (pp30) REVERT: E 65 LYS cc_start: 0.9024 (pttt) cc_final: 0.8721 (pttt) REVERT: F 11 HIS cc_start: 0.9224 (t-90) cc_final: 0.8537 (t-90) REVERT: F 75 GLU cc_start: 0.9348 (pt0) cc_final: 0.9088 (pp20) REVERT: G 8 GLN cc_start: 0.8279 (pt0) cc_final: 0.7616 (pp30) REVERT: H 12 ARG cc_start: 0.8716 (mpt-90) cc_final: 0.8503 (mpt-90) REVERT: H 58 LEU cc_start: 0.9144 (tp) cc_final: 0.8755 (tp) REVERT: I 99 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8547 (mttm) REVERT: I 106 ASP cc_start: 0.8531 (t70) cc_final: 0.8289 (t0) REVERT: J 42 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7701 (mm) REVERT: J 65 TYR cc_start: 0.6575 (m-80) cc_final: 0.5136 (m-80) REVERT: J 81 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8271 (mp0) REVERT: K 13 LYS cc_start: 0.8881 (tptp) cc_final: 0.8512 (mtmt) REVERT: L 23 LEU cc_start: 0.8848 (tp) cc_final: 0.8593 (tt) REVERT: M 71 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8971 (mm-30) REVERT: M 90 HIS cc_start: 0.8941 (m-70) cc_final: 0.8437 (m170) REVERT: M 92 ARG cc_start: 0.9207 (mtp85) cc_final: 0.8831 (ptt180) REVERT: M 101 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8840 (p) REVERT: N 38 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8363 (tp30) REVERT: N 84 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8208 (ttm-80) REVERT: O 10 ILE cc_start: 0.9249 (mt) cc_final: 0.8986 (tt) REVERT: O 41 HIS cc_start: 0.7514 (t70) cc_final: 0.7263 (t-90) REVERT: O 47 LYS cc_start: 0.7953 (pttt) cc_final: 0.7698 (pttm) REVERT: Q 35 LYS cc_start: 0.9187 (tptp) cc_final: 0.8979 (tptp) REVERT: S 65 MET cc_start: 0.8651 (mtm) cc_final: 0.8272 (ptp) REVERT: T 27 MET cc_start: 0.9396 (mmm) cc_final: 0.8865 (mmm) REVERT: T 56 ILE cc_start: 0.8722 (tp) cc_final: 0.8380 (tp) REVERT: U 20 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6820 (mtm-85) REVERT: U 57 LYS cc_start: 0.8444 (mmpt) cc_final: 0.7738 (tmtt) REVERT: 03 53 ARG cc_start: 0.6764 (mpt180) cc_final: 0.6414 (mmt90) REVERT: Z 13 ASN cc_start: 0.6488 (OUTLIER) cc_final: 0.6219 (p0) REVERT: Z 112 MET cc_start: 0.2997 (mtp) cc_final: 0.2644 (mpp) REVERT: Z 123 ARG cc_start: 0.8129 (tpm170) cc_final: 0.6941 (tmt170) REVERT: Z 155 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7428 (tm-30) REVERT: Z 159 GLN cc_start: 0.7393 (tt0) cc_final: 0.6864 (tt0) outliers start: 372 outliers final: 249 residues processed: 1119 average time/residue: 1.3346 time to fit residues: 2656.4866 Evaluate side-chains 1055 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 788 time to evaluate : 6.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 53 ILE Chi-restraints excluded: chain 04 residue 64 VAL Chi-restraints excluded: chain 04 residue 87 SER Chi-restraints excluded: chain 04 residue 132 ARG Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 266 ILE Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 14 ILE Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 40 LEU Chi-restraints excluded: chain 05 residue 51 THR Chi-restraints excluded: chain 05 residue 77 ARG Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 136 ASN Chi-restraints excluded: chain 05 residue 161 MET Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 203 VAL Chi-restraints excluded: chain 06 residue 126 VAL Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 07 residue 3 LEU Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 20 ASN Chi-restraints excluded: chain 07 residue 25 MET Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 90 LEU Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 07 residue 172 PHE Chi-restraints excluded: chain 07 residue 173 ASP Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 106 LEU Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 6 LEU Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 19 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 70 GLU Chi-restraints excluded: chain 09 residue 80 ILE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 111 THR Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 19 ASP Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 13 residue 3 GLN Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 13 residue 109 SER Chi-restraints excluded: chain 13 residue 111 LYS Chi-restraints excluded: chain 14 residue 81 ASP Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 14 residue 135 ILE Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 29 VAL Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 73 ASN Chi-restraints excluded: chain 16 residue 75 ILE Chi-restraints excluded: chain 16 residue 120 GLU Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 17 residue 94 ARG Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 4 ILE Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 98 TYR Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 39 ILE Chi-restraints excluded: chain 19 residue 75 TYR Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 19 residue 99 VAL Chi-restraints excluded: chain 20 residue 13 ARG Chi-restraints excluded: chain 20 residue 49 ILE Chi-restraints excluded: chain 20 residue 55 ASP Chi-restraints excluded: chain 20 residue 94 THR Chi-restraints excluded: chain 20 residue 95 ASP Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 71 VAL Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 40 LEU Chi-restraints excluded: chain 23 residue 65 GLN Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 12 GLN Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 45 ASP Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 75 PHE Chi-restraints excluded: chain 25 residue 76 ILE Chi-restraints excluded: chain 26 residue 10 ARG Chi-restraints excluded: chain 26 residue 16 ASN Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 16 LEU Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 29 residue 4 ASP Chi-restraints excluded: chain 29 residue 22 MET Chi-restraints excluded: chain 29 residue 35 ASP Chi-restraints excluded: chain 29 residue 48 GLN Chi-restraints excluded: chain 29 residue 50 ASP Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 21 LEU Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 8 SER Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 38 GLU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 84 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 71 SER Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 11 PHE Chi-restraints excluded: chain U residue 20 ARG Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 69 THR Chi-restraints excluded: chain 03 residue 192 LEU Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 13 ASN Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 108 THR Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 320 THR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 886 optimal weight: 30.0000 chunk 604 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 792 optimal weight: 20.0000 chunk 439 optimal weight: 9.9990 chunk 908 optimal weight: 20.0000 chunk 735 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 543 optimal weight: 5.9990 chunk 955 optimal weight: 50.0000 chunk 268 optimal weight: 30.0000 overall best weight: 12.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 225 ASN ** 06 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 88 HIS ** 13 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 38 GLN ** 16 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 26 16 ASN 28 48 ASN 32 6 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS ** 03 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 166780 Z= 0.345 Angle : 0.766 16.237 249021 Z= 0.393 Chirality : 0.042 0.354 31775 Planarity : 0.006 0.062 13713 Dihedral : 24.018 179.158 82265 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 33.19 Ramachandran Plot: Outliers : 0.38 % Allowed : 14.11 % Favored : 85.52 % Rotamer: Outliers : 7.42 % Allowed : 21.42 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.10), residues: 6366 helix: -1.12 (0.11), residues: 1933 sheet: -2.29 (0.15), residues: 974 loop : -2.71 (0.10), residues: 3459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 17 HIS 0.011 0.002 HIS D 197 PHE 0.027 0.003 PHE Z 162 TYR 0.035 0.003 TYR E 127 ARG 0.044 0.001 ARG12 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 392 poor density : 827 time to evaluate : 6.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 131 MET cc_start: 0.8643 (mpp) cc_final: 0.8362 (mpp) REVERT: 04 176 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8950 (tpt170) REVERT: 05 42 ASN cc_start: 0.8970 (m110) cc_final: 0.8110 (t0) REVERT: 05 90 PHE cc_start: 0.8093 (m-80) cc_final: 0.7700 (m-10) REVERT: 05 148 GLN cc_start: 0.8376 (mp10) cc_final: 0.7989 (mt0) REVERT: 06 100 MET cc_start: 0.8916 (mtt) cc_final: 0.8293 (mmt) REVERT: 06 153 LEU cc_start: 0.7517 (tp) cc_final: 0.6910 (mt) REVERT: 06 176 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8344 (p0) REVERT: 07 9 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.6967 (p0) REVERT: 07 25 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: 07 80 GLN cc_start: 0.8292 (tp40) cc_final: 0.7953 (tp-100) REVERT: 07 82 TYR cc_start: 0.8830 (t80) cc_final: 0.8454 (t80) REVERT: 07 89 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7869 (p) REVERT: 09 8 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8270 (tptp) REVERT: 09 12 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8332 (pp) REVERT: 09 35 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7844 (mtmm) REVERT: 10 52 MET cc_start: 0.1156 (ttp) cc_final: 0.0179 (mtt) REVERT: 10 86 MET cc_start: -0.1302 (mmt) cc_final: -0.1846 (mmt) REVERT: 10 122 GLN cc_start: 0.7928 (pm20) cc_final: 0.7472 (tm-30) REVERT: 11 9 LYS cc_start: 0.3962 (OUTLIER) cc_final: 0.3631 (ttpp) REVERT: 11 59 THR cc_start: 0.7226 (m) cc_final: 0.7016 (m) REVERT: 11 116 MET cc_start: 0.3359 (mmp) cc_final: 0.2348 (tpp) REVERT: 11 135 MET cc_start: 0.4776 (tpp) cc_final: 0.3881 (tpp) REVERT: 13 49 ARG cc_start: 0.8481 (mmp-170) cc_final: 0.8213 (mmp-170) REVERT: 13 111 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8258 (ptpp) REVERT: 14 115 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6430 (tm-30) REVERT: 14 144 GLU cc_start: 0.6674 (pt0) cc_final: 0.6226 (mm-30) REVERT: 15 60 GLN cc_start: 0.8504 (pp30) cc_final: 0.8006 (pp30) REVERT: 16 18 GLN cc_start: 0.9079 (tt0) cc_final: 0.8235 (tm-30) REVERT: 16 20 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8445 (ppp) REVERT: 16 75 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9188 (mm) REVERT: 17 94 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8187 (ttp-170) REVERT: 18 12 MET cc_start: 0.8682 (ttp) cc_final: 0.8418 (ttm) REVERT: 18 43 GLU cc_start: 0.7619 (tp30) cc_final: 0.7303 (tp30) REVERT: 18 51 ASN cc_start: 0.7087 (t0) cc_final: 0.6822 (t0) REVERT: 20 13 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7674 (ttp80) REVERT: 20 80 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7922 (ptp-110) REVERT: 20 82 HIS cc_start: 0.8448 (t-90) cc_final: 0.8020 (t-170) REVERT: 20 94 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8922 (m) REVERT: 21 31 GLN cc_start: 0.9269 (mt0) cc_final: 0.8975 (pp30) REVERT: 21 52 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8403 (pt0) REVERT: 22 1 MET cc_start: 0.5229 (ptp) cc_final: 0.4942 (mtt) REVERT: 22 42 GLU cc_start: 0.8719 (mp0) cc_final: 0.8494 (mp0) REVERT: 23 17 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.7827 (t0) REVERT: 23 18 LYS cc_start: 0.9579 (tmmt) cc_final: 0.9326 (mtpt) REVERT: 24 29 ILE cc_start: 0.8303 (tt) cc_final: 0.7962 (pt) REVERT: 24 45 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8389 (t0) REVERT: 25 40 LYS cc_start: 0.8692 (mttt) cc_final: 0.7790 (mttp) REVERT: 25 64 LYS cc_start: 0.9046 (tppp) cc_final: 0.8820 (tppt) REVERT: 26 69 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8681 (mt-10) REVERT: 27 59 GLU cc_start: 0.9424 (tt0) cc_final: 0.9121 (mt-10) REVERT: 28 18 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8267 (mmtt) REVERT: 28 20 LYS cc_start: 0.9334 (mtmm) cc_final: 0.9110 (mtmm) REVERT: 29 1 MET cc_start: 0.7517 (mtt) cc_final: 0.7047 (ppp) REVERT: 30 14 MET cc_start: 0.9005 (mtp) cc_final: 0.8663 (ptp) REVERT: 30 27 LEU cc_start: 0.9014 (mp) cc_final: 0.8604 (mt) REVERT: 30 45 ASP cc_start: 0.9149 (m-30) cc_final: 0.8282 (t0) REVERT: 32 22 MET cc_start: 0.8446 (mmm) cc_final: 0.7971 (tpp) REVERT: 34 2 LYS cc_start: 0.7125 (mmtt) cc_final: 0.6733 (mmtt) REVERT: B 19 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7696 (t) REVERT: B 26 MET cc_start: 0.7089 (mtp) cc_final: 0.5896 (tmm) REVERT: B 36 LYS cc_start: 0.7382 (mttp) cc_final: 0.6624 (tptt) REVERT: B 37 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7846 (m) REVERT: B 93 HIS cc_start: 0.8490 (m170) cc_final: 0.7887 (m-70) REVERT: B 94 ARG cc_start: 0.7841 (mpt180) cc_final: 0.6984 (tpt170) REVERT: B 119 GLN cc_start: 0.6721 (OUTLIER) cc_final: 0.6465 (pp30) REVERT: C 128 MET cc_start: 0.8349 (tpt) cc_final: 0.8102 (tpp) REVERT: C 180 ASP cc_start: 0.9024 (t70) cc_final: 0.8596 (p0) REVERT: C 182 ASP cc_start: 0.8575 (t0) cc_final: 0.8261 (t0) REVERT: D 3 TYR cc_start: 0.7942 (t80) cc_final: 0.7479 (t80) REVERT: D 46 ARG cc_start: 0.6886 (tpm170) cc_final: 0.6125 (tpm170) REVERT: D 135 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8046 (tm-30) REVERT: D 196 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7374 (pp20) REVERT: E 12 GLU cc_start: 0.6527 (pt0) cc_final: 0.6219 (pm20) REVERT: E 60 GLN cc_start: 0.9044 (pt0) cc_final: 0.8785 (pp30) REVERT: E 65 LYS cc_start: 0.9058 (pttt) cc_final: 0.8715 (pttt) REVERT: E 144 GLU cc_start: 0.8829 (tp30) cc_final: 0.8473 (tp30) REVERT: F 1 MET cc_start: 0.8158 (mtm) cc_final: 0.7318 (ttp) REVERT: F 11 HIS cc_start: 0.9213 (t-90) cc_final: 0.8517 (t-90) REVERT: F 62 MET cc_start: 0.9140 (mmm) cc_final: 0.8853 (mmm) REVERT: F 75 GLU cc_start: 0.9408 (pt0) cc_final: 0.9132 (pp20) REVERT: G 8 GLN cc_start: 0.8367 (pt0) cc_final: 0.7667 (pp30) REVERT: G 46 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8904 (mm) REVERT: G 143 MET cc_start: 0.7466 (mmt) cc_final: 0.6951 (mmt) REVERT: H 26 MET cc_start: 0.7920 (ppp) cc_final: 0.7592 (ppp) REVERT: I 99 LYS cc_start: 0.9098 (ttpt) cc_final: 0.8584 (mttm) REVERT: I 106 ASP cc_start: 0.8523 (t70) cc_final: 0.8296 (t0) REVERT: J 42 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7973 (mm) REVERT: J 65 TYR cc_start: 0.6627 (m-80) cc_final: 0.6251 (m-80) REVERT: J 81 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8262 (mp0) REVERT: K 13 LYS cc_start: 0.8895 (tptp) cc_final: 0.8535 (mtmt) REVERT: M 71 GLU cc_start: 0.9395 (mt-10) cc_final: 0.8954 (mm-30) REVERT: M 90 HIS cc_start: 0.9021 (m-70) cc_final: 0.8491 (m170) REVERT: M 92 ARG cc_start: 0.9195 (mtp85) cc_final: 0.8833 (ptt180) REVERT: M 101 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8750 (p) REVERT: N 38 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8315 (tp30) REVERT: O 10 ILE cc_start: 0.9247 (mt) cc_final: 0.9008 (tt) REVERT: O 47 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7755 (pttm) REVERT: Q 35 LYS cc_start: 0.9176 (tptp) cc_final: 0.8870 (tptt) REVERT: S 65 MET cc_start: 0.8730 (mtm) cc_final: 0.8234 (ptm) REVERT: U 20 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6864 (mtm-85) REVERT: U 57 LYS cc_start: 0.8400 (mmpt) cc_final: 0.7624 (tmtt) REVERT: Z 123 ARG cc_start: 0.8176 (tpm170) cc_final: 0.7451 (mtt90) REVERT: Z 155 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7435 (tm-30) REVERT: Z 159 GLN cc_start: 0.7225 (tt0) cc_final: 0.6862 (tt0) REVERT: Z 215 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7098 (tt0) outliers start: 392 outliers final: 271 residues processed: 1110 average time/residue: 1.4422 time to fit residues: 2817.2246 Evaluate side-chains 1062 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 765 time to evaluate : 6.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 53 ILE Chi-restraints excluded: chain 04 residue 87 SER Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 132 ARG Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 176 ARG Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 266 ILE Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 51 THR Chi-restraints excluded: chain 05 residue 77 ARG Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 136 ASN Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 203 VAL Chi-restraints excluded: chain 06 residue 1 MET Chi-restraints excluded: chain 06 residue 84 THR Chi-restraints excluded: chain 06 residue 113 VAL Chi-restraints excluded: chain 06 residue 126 VAL Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 06 residue 176 ASP Chi-restraints excluded: chain 07 residue 3 LEU Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 20 ASN Chi-restraints excluded: chain 07 residue 25 MET Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 90 LEU Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 07 residue 172 PHE Chi-restraints excluded: chain 07 residue 173 ASP Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 16 VAL Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 106 LEU Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 19 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 62 LEU Chi-restraints excluded: chain 09 residue 80 ILE Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 9 LYS Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 19 ASP Chi-restraints excluded: chain 12 residue 60 ASP Chi-restraints excluded: chain 13 residue 3 GLN Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 109 SER Chi-restraints excluded: chain 13 residue 111 LYS Chi-restraints excluded: chain 13 residue 118 LEU Chi-restraints excluded: chain 14 residue 81 ASP Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 14 residue 135 ILE Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 29 VAL Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 75 ILE Chi-restraints excluded: chain 16 residue 120 GLU Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 17 residue 94 ARG Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 4 ILE Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 32 VAL Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 80 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 98 TYR Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 19 residue 39 ILE Chi-restraints excluded: chain 19 residue 46 TYR Chi-restraints excluded: chain 19 residue 75 TYR Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 13 ARG Chi-restraints excluded: chain 20 residue 15 SER Chi-restraints excluded: chain 20 residue 49 ILE Chi-restraints excluded: chain 20 residue 80 ARG Chi-restraints excluded: chain 20 residue 94 THR Chi-restraints excluded: chain 20 residue 95 ASP Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 42 LYS Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 71 VAL Chi-restraints excluded: chain 22 residue 25 GLU Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 40 LEU Chi-restraints excluded: chain 23 residue 58 VAL Chi-restraints excluded: chain 23 residue 65 GLN Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 45 ASP Chi-restraints excluded: chain 24 residue 61 LEU Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 75 PHE Chi-restraints excluded: chain 25 residue 76 ILE Chi-restraints excluded: chain 26 residue 10 ARG Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 16 LEU Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 4 ASP Chi-restraints excluded: chain 29 residue 21 VAL Chi-restraints excluded: chain 29 residue 35 ASP Chi-restraints excluded: chain 29 residue 47 LYS Chi-restraints excluded: chain 29 residue 48 GLN Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 21 LEU Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 8 SER Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 4 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 38 GLU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 84 ARG Chi-restraints excluded: chain N residue 100 TRP Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 71 SER Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 11 PHE Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 20 ARG Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 22 ASP Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 69 THR Chi-restraints excluded: chain 03 residue 192 LEU Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain 03 residue 225 ASP Chi-restraints excluded: chain Z residue 65 SER Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 108 THR Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 320 THR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 358 optimal weight: 20.0000 chunk 958 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 624 optimal weight: 30.0000 chunk 262 optimal weight: 30.0000 chunk 1065 optimal weight: 5.9990 chunk 884 optimal weight: 30.0000 chunk 493 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 352 optimal weight: 20.0000 chunk 559 optimal weight: 6.9990 overall best weight: 10.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 06 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 195 GLN ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 126 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 88 HIS ** 13 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 26 16 ASN 28 48 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN O 39 GLN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 60 GLN ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS ** 03 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 166780 Z= 0.298 Angle : 0.722 16.661 249021 Z= 0.372 Chirality : 0.040 0.412 31775 Planarity : 0.005 0.051 13713 Dihedral : 24.078 178.932 82263 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 30.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.94 % Favored : 86.68 % Rotamer: Outliers : 7.28 % Allowed : 22.78 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.10), residues: 6366 helix: -0.97 (0.11), residues: 1939 sheet: -2.22 (0.15), residues: 984 loop : -2.61 (0.10), residues: 3443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 17 HIS 0.010 0.002 HIS D 197 PHE 0.032 0.002 PHE15 117 TYR 0.027 0.002 TYR O 77 ARG 0.018 0.001 ARG12 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 385 poor density : 804 time to evaluate : 6.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 131 MET cc_start: 0.8606 (mpp) cc_final: 0.8361 (mpp) REVERT: 05 11 MET cc_start: 0.6918 (tpt) cc_final: 0.6518 (tpt) REVERT: 05 42 ASN cc_start: 0.8961 (m110) cc_final: 0.8127 (t0) REVERT: 05 90 PHE cc_start: 0.8073 (m-80) cc_final: 0.7734 (m-10) REVERT: 05 148 GLN cc_start: 0.8334 (mp10) cc_final: 0.7979 (mt0) REVERT: 06 100 MET cc_start: 0.8881 (mtt) cc_final: 0.8255 (mmt) REVERT: 06 153 LEU cc_start: 0.7526 (tp) cc_final: 0.6905 (mt) REVERT: 06 176 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8311 (p0) REVERT: 07 9 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7035 (p0) REVERT: 07 82 TYR cc_start: 0.8764 (t80) cc_final: 0.8391 (t80) REVERT: 07 89 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7694 (p) REVERT: 09 8 LYS cc_start: 0.9023 (mmmt) cc_final: 0.8493 (tptp) REVERT: 09 12 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8355 (pp) REVERT: 10 52 MET cc_start: 0.1312 (ttp) cc_final: 0.0389 (mtt) REVERT: 10 86 MET cc_start: -0.1206 (mmt) cc_final: -0.1678 (mmt) REVERT: 10 99 PHE cc_start: 0.7290 (m-10) cc_final: 0.6801 (m-10) REVERT: 10 122 GLN cc_start: 0.7851 (pm20) cc_final: 0.7451 (tm-30) REVERT: 11 64 ARG cc_start: 0.7434 (mmm-85) cc_final: 0.6656 (mmp80) REVERT: 11 116 MET cc_start: 0.3010 (mmp) cc_final: 0.1882 (tpp) REVERT: 11 135 MET cc_start: 0.4703 (tpp) cc_final: 0.4028 (tpp) REVERT: 13 49 ARG cc_start: 0.8514 (mmp-170) cc_final: 0.8229 (mmp-170) REVERT: 13 58 LEU cc_start: 0.8409 (mt) cc_final: 0.8203 (mt) REVERT: 13 93 GLN cc_start: 0.8145 (mp10) cc_final: 0.7903 (mp10) REVERT: 13 111 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8175 (ptpp) REVERT: 14 51 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8707 (mt-10) REVERT: 14 55 MET cc_start: 0.8633 (mmm) cc_final: 0.8417 (mmm) REVERT: 14 115 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6531 (tm-30) REVERT: 14 144 GLU cc_start: 0.6671 (pt0) cc_final: 0.6202 (mm-30) REVERT: 15 60 GLN cc_start: 0.8448 (pp30) cc_final: 0.7976 (pp30) REVERT: 16 18 GLN cc_start: 0.9059 (tt0) cc_final: 0.8214 (tm-30) REVERT: 16 20 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8418 (ppp) REVERT: 16 75 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9136 (mm) REVERT: 17 94 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8005 (ttp-170) REVERT: 18 12 MET cc_start: 0.8637 (ttp) cc_final: 0.8355 (ttm) REVERT: 18 51 ASN cc_start: 0.7055 (t0) cc_final: 0.6780 (t0) REVERT: 20 82 HIS cc_start: 0.8370 (t-90) cc_final: 0.7988 (t-170) REVERT: 20 94 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8971 (m) REVERT: 21 31 GLN cc_start: 0.9268 (mt0) cc_final: 0.8977 (pp30) REVERT: 22 42 GLU cc_start: 0.8736 (mp0) cc_final: 0.8499 (mp0) REVERT: 23 17 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.7752 (t0) REVERT: 23 18 LYS cc_start: 0.9594 (tmmt) cc_final: 0.9345 (ttmt) REVERT: 24 29 ILE cc_start: 0.8261 (tt) cc_final: 0.7919 (pt) REVERT: 24 45 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8368 (t0) REVERT: 24 48 MET cc_start: 0.8807 (tpp) cc_final: 0.8406 (tpp) REVERT: 25 40 LYS cc_start: 0.8704 (mttt) cc_final: 0.7752 (mttp) REVERT: 25 64 LYS cc_start: 0.9030 (tppp) cc_final: 0.8724 (tppt) REVERT: 26 69 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8697 (mt-10) REVERT: 27 59 GLU cc_start: 0.9449 (tt0) cc_final: 0.9138 (mt-10) REVERT: 28 18 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8193 (mmtt) REVERT: 28 20 LYS cc_start: 0.9340 (mtmm) cc_final: 0.9104 (mtmm) REVERT: 29 1 MET cc_start: 0.7605 (mtt) cc_final: 0.7096 (ppp) REVERT: 30 27 LEU cc_start: 0.8933 (mp) cc_final: 0.8610 (mt) REVERT: 30 45 ASP cc_start: 0.9166 (m-30) cc_final: 0.8230 (t0) REVERT: 32 8 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8068 (p) REVERT: 32 22 MET cc_start: 0.8483 (mmm) cc_final: 0.8178 (tpp) REVERT: B 37 VAL cc_start: 0.8087 (OUTLIER) cc_final: 0.7873 (t) REVERT: B 93 HIS cc_start: 0.8506 (m170) cc_final: 0.7893 (m-70) REVERT: B 94 ARG cc_start: 0.7822 (mpt180) cc_final: 0.6943 (tpt170) REVERT: B 187 ASP cc_start: 0.3794 (OUTLIER) cc_final: 0.3397 (m-30) REVERT: C 122 GLN cc_start: 0.9092 (mt0) cc_final: 0.8880 (mt0) REVERT: C 128 MET cc_start: 0.8237 (tpt) cc_final: 0.7923 (tpt) REVERT: C 180 ASP cc_start: 0.9013 (t70) cc_final: 0.8592 (p0) REVERT: C 182 ASP cc_start: 0.8567 (t0) cc_final: 0.8250 (t0) REVERT: D 3 TYR cc_start: 0.7942 (t80) cc_final: 0.7478 (t80) REVERT: D 21 LYS cc_start: 0.7716 (tttt) cc_final: 0.7400 (ttmm) REVERT: D 32 LYS cc_start: 0.8772 (mttt) cc_final: 0.8207 (ttpt) REVERT: D 46 ARG cc_start: 0.6901 (tpm170) cc_final: 0.6164 (tpm170) REVERT: D 135 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7906 (tm-30) REVERT: D 196 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: E 12 GLU cc_start: 0.6441 (pt0) cc_final: 0.6171 (pm20) REVERT: E 60 GLN cc_start: 0.9013 (pt0) cc_final: 0.8759 (pp30) REVERT: E 65 LYS cc_start: 0.9082 (pttt) cc_final: 0.8686 (pttt) REVERT: E 144 GLU cc_start: 0.8897 (tp30) cc_final: 0.8528 (tp30) REVERT: F 11 HIS cc_start: 0.9205 (t-90) cc_final: 0.8504 (t-90) REVERT: F 14 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8181 (tp40) REVERT: F 75 GLU cc_start: 0.9417 (pt0) cc_final: 0.9130 (pp20) REVERT: G 8 GLN cc_start: 0.8340 (pt0) cc_final: 0.7571 (pp30) REVERT: G 143 MET cc_start: 0.7389 (mmt) cc_final: 0.7008 (mmt) REVERT: H 26 MET cc_start: 0.7759 (ppp) cc_final: 0.7468 (ppp) REVERT: I 106 ASP cc_start: 0.8459 (t70) cc_final: 0.8246 (t0) REVERT: J 24 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8797 (tt0) REVERT: J 42 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7889 (mm) REVERT: J 65 TYR cc_start: 0.6300 (m-80) cc_final: 0.5047 (m-80) REVERT: J 75 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: J 81 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8251 (mp0) REVERT: K 13 LYS cc_start: 0.8900 (tptp) cc_final: 0.8534 (mtmt) REVERT: L 23 LEU cc_start: 0.8857 (tp) cc_final: 0.8473 (tt) REVERT: M 90 HIS cc_start: 0.8987 (m-70) cc_final: 0.8446 (m170) REVERT: M 92 ARG cc_start: 0.9215 (mtp85) cc_final: 0.8855 (ptt180) REVERT: N 38 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8285 (tp30) REVERT: N 64 ARG cc_start: 0.6287 (OUTLIER) cc_final: 0.6023 (ttt180) REVERT: N 84 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8132 (ttm-80) REVERT: O 10 ILE cc_start: 0.9237 (mt) cc_final: 0.8990 (tt) REVERT: O 47 LYS cc_start: 0.8008 (pttt) cc_final: 0.7738 (pttm) REVERT: Q 35 LYS cc_start: 0.9189 (tptp) cc_final: 0.8869 (tptt) REVERT: S 65 MET cc_start: 0.8773 (mtm) cc_final: 0.8318 (ptp) REVERT: T 27 MET cc_start: 0.9487 (mmm) cc_final: 0.9105 (mmm) REVERT: U 20 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6826 (mtm-85) REVERT: U 30 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: U 57 LYS cc_start: 0.8401 (mmpt) cc_final: 0.7616 (tmtt) REVERT: 03 165 ASN cc_start: 0.6261 (OUTLIER) cc_final: 0.5965 (p0) REVERT: 03 218 MET cc_start: 0.7328 (mtp) cc_final: 0.6271 (mtp) REVERT: Z 13 ASN cc_start: 0.6290 (p0) cc_final: 0.6031 (p0) REVERT: Z 155 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7451 (tm-30) REVERT: Z 159 GLN cc_start: 0.7352 (tt0) cc_final: 0.6896 (tt0) REVERT: Z 215 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7090 (tt0) outliers start: 385 outliers final: 286 residues processed: 1078 average time/residue: 1.4634 time to fit residues: 2789.3912 Evaluate side-chains 1059 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 749 time to evaluate : 6.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 53 ILE Chi-restraints excluded: chain 04 residue 64 VAL Chi-restraints excluded: chain 04 residue 87 SER Chi-restraints excluded: chain 04 residue 97 ASP Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 132 ARG Chi-restraints excluded: chain 04 residue 194 VAL Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 266 ILE Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 25 THR Chi-restraints excluded: chain 05 residue 51 THR Chi-restraints excluded: chain 05 residue 77 ARG Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 203 VAL Chi-restraints excluded: chain 06 residue 113 VAL Chi-restraints excluded: chain 06 residue 126 VAL Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 06 residue 176 ASP Chi-restraints excluded: chain 07 residue 3 LEU Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 20 ASN Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 90 LEU Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 07 residue 172 PHE Chi-restraints excluded: chain 07 residue 173 ASP Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 16 VAL Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 106 LEU Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 61 VAL Chi-restraints excluded: chain 09 residue 62 LEU Chi-restraints excluded: chain 09 residue 80 ILE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 111 THR Chi-restraints excluded: chain 11 residue 137 LEU Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 19 ASP Chi-restraints excluded: chain 12 residue 45 THR Chi-restraints excluded: chain 12 residue 60 ASP Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 109 LEU Chi-restraints excluded: chain 13 residue 3 GLN Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 95 ILE Chi-restraints excluded: chain 13 residue 108 ARG Chi-restraints excluded: chain 13 residue 109 SER Chi-restraints excluded: chain 13 residue 111 LYS Chi-restraints excluded: chain 13 residue 118 LEU Chi-restraints excluded: chain 14 residue 81 ASP Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 14 residue 135 ILE Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 29 VAL Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 75 ILE Chi-restraints excluded: chain 16 residue 120 GLU Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 24 THR Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 17 residue 94 ARG Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 4 ILE Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 80 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 39 ILE Chi-restraints excluded: chain 19 residue 43 GLN Chi-restraints excluded: chain 19 residue 75 TYR Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 13 ARG Chi-restraints excluded: chain 20 residue 15 SER Chi-restraints excluded: chain 20 residue 20 VAL Chi-restraints excluded: chain 20 residue 49 ILE Chi-restraints excluded: chain 20 residue 55 ASP Chi-restraints excluded: chain 20 residue 80 ARG Chi-restraints excluded: chain 20 residue 94 THR Chi-restraints excluded: chain 20 residue 95 ASP Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 71 VAL Chi-restraints excluded: chain 22 residue 25 GLU Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 40 LEU Chi-restraints excluded: chain 23 residue 58 VAL Chi-restraints excluded: chain 23 residue 65 GLN Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 45 ASP Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 75 PHE Chi-restraints excluded: chain 25 residue 76 ILE Chi-restraints excluded: chain 26 residue 10 ARG Chi-restraints excluded: chain 26 residue 16 ASN Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 67 LEU Chi-restraints excluded: chain 26 residue 70 LEU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 16 LEU Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 4 ASP Chi-restraints excluded: chain 29 residue 35 ASP Chi-restraints excluded: chain 29 residue 47 LYS Chi-restraints excluded: chain 29 residue 48 GLN Chi-restraints excluded: chain 29 residue 50 ASP Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 21 LEU Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 8 SER Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 4 LYS Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 58 ILE Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 38 GLU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 84 ARG Chi-restraints excluded: chain N residue 100 TRP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 71 SER Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain T residue 74 HIS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 11 PHE Chi-restraints excluded: chain U residue 20 ARG Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 22 ASP Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 69 THR Chi-restraints excluded: chain 03 residue 165 ASN Chi-restraints excluded: chain 03 residue 178 VAL Chi-restraints excluded: chain 03 residue 192 LEU Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain 03 residue 225 ASP Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 65 SER Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 108 THR Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Z residue 320 THR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 1027 optimal weight: 30.0000 chunk 120 optimal weight: 2.9990 chunk 606 optimal weight: 30.0000 chunk 777 optimal weight: 20.0000 chunk 602 optimal weight: 30.0000 chunk 896 optimal weight: 30.0000 chunk 594 optimal weight: 30.0000 chunk 1061 optimal weight: 50.0000 chunk 664 optimal weight: 20.0000 chunk 646 optimal weight: 30.0000 chunk 489 optimal weight: 30.0000 overall best weight: 20.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 06 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 126 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 18 51 ASN ** 19 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN 28 48 ASN 31 44 GLN ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN O 49 HIS ** Q 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 ASN ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS 03 20 GLN ** 03 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 329 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.152 166780 Z= 0.554 Angle : 1.006 17.483 249021 Z= 0.506 Chirality : 0.051 0.431 31775 Planarity : 0.008 0.084 13713 Dihedral : 24.582 178.744 82263 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 48.78 Ramachandran Plot: Outliers : 0.41 % Allowed : 16.37 % Favored : 83.22 % Rotamer: Outliers : 8.38 % Allowed : 23.58 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.09), residues: 6366 helix: -1.58 (0.11), residues: 1940 sheet: -2.34 (0.15), residues: 940 loop : -2.97 (0.09), residues: 3486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 17 HIS 0.020 0.003 HIS T 74 PHE 0.046 0.004 PHE15 117 TYR 0.035 0.003 TYR E 127 ARG 0.015 0.001 ARG08 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 443 poor density : 707 time to evaluate : 6.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 202 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7402 (mmt-90) REVERT: 05 11 MET cc_start: 0.7024 (tpt) cc_final: 0.6415 (tpt) REVERT: 05 42 ASN cc_start: 0.8913 (m110) cc_final: 0.8049 (t0) REVERT: 05 90 PHE cc_start: 0.8146 (m-80) cc_final: 0.7819 (m-10) REVERT: 05 148 GLN cc_start: 0.8643 (mp10) cc_final: 0.8124 (mt0) REVERT: 06 100 MET cc_start: 0.8964 (mtt) cc_final: 0.8390 (mmt) REVERT: 07 9 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.6877 (p0) REVERT: 07 82 TYR cc_start: 0.8872 (t80) cc_final: 0.8651 (t80) REVERT: 09 8 LYS cc_start: 0.9171 (mmmt) cc_final: 0.8428 (tptp) REVERT: 09 12 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8423 (pp) REVERT: 10 52 MET cc_start: 0.1554 (ttp) cc_final: 0.0671 (mtt) REVERT: 10 86 MET cc_start: -0.0419 (mmt) cc_final: -0.0979 (mmt) REVERT: 10 99 PHE cc_start: 0.7372 (m-10) cc_final: 0.6881 (m-10) REVERT: 11 116 MET cc_start: 0.3223 (mmp) cc_final: 0.1605 (ttm) REVERT: 11 135 MET cc_start: 0.4653 (tpp) cc_final: 0.4253 (tpp) REVERT: 12 131 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.7825 (p0) REVERT: 13 22 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7981 (pt) REVERT: 13 49 ARG cc_start: 0.8524 (mmp-170) cc_final: 0.8193 (mmp-170) REVERT: 13 93 GLN cc_start: 0.8431 (mp10) cc_final: 0.8101 (mp10) REVERT: 13 111 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8048 (ptpp) REVERT: 14 77 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8482 (tp) REVERT: 14 115 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6541 (tm-30) REVERT: 14 144 GLU cc_start: 0.7113 (pt0) cc_final: 0.6765 (mm-30) REVERT: 16 18 GLN cc_start: 0.9133 (tt0) cc_final: 0.8253 (tm-30) REVERT: 16 75 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9203 (mm) REVERT: 17 94 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8050 (ttp-170) REVERT: 18 12 MET cc_start: 0.8700 (ttp) cc_final: 0.8363 (ttm) REVERT: 20 13 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8181 (ttt90) REVERT: 20 80 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7532 (ptp-110) REVERT: 20 82 HIS cc_start: 0.8442 (t-90) cc_final: 0.8001 (t-170) REVERT: 21 31 GLN cc_start: 0.9352 (mt0) cc_final: 0.8973 (pp30) REVERT: 21 52 GLU cc_start: 0.8300 (pt0) cc_final: 0.7974 (pp20) REVERT: 22 1 MET cc_start: 0.6093 (mtt) cc_final: 0.5335 (mtt) REVERT: 23 18 LYS cc_start: 0.9614 (tmmt) cc_final: 0.9367 (ttmt) REVERT: 25 40 LYS cc_start: 0.8731 (mttt) cc_final: 0.7836 (mtmm) REVERT: 25 64 LYS cc_start: 0.9048 (tppp) cc_final: 0.8839 (tppt) REVERT: 26 69 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8700 (mt-10) REVERT: 27 59 GLU cc_start: 0.9471 (tt0) cc_final: 0.9136 (mt-10) REVERT: 28 18 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8382 (mmtt) REVERT: 29 1 MET cc_start: 0.7615 (mtt) cc_final: 0.7295 (tmm) REVERT: 30 27 LEU cc_start: 0.8992 (mp) cc_final: 0.8735 (mt) REVERT: B 93 HIS cc_start: 0.8503 (m170) cc_final: 0.7849 (m-70) REVERT: B 94 ARG cc_start: 0.8021 (mpt180) cc_final: 0.7106 (tpt170) REVERT: C 17 TRP cc_start: 0.8028 (m-10) cc_final: 0.7774 (m-10) REVERT: C 128 MET cc_start: 0.8235 (tpt) cc_final: 0.7967 (tpp) REVERT: C 169 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8343 (tm-30) REVERT: C 180 ASP cc_start: 0.8953 (t70) cc_final: 0.8357 (p0) REVERT: C 182 ASP cc_start: 0.8735 (t0) cc_final: 0.8372 (t0) REVERT: D 3 TYR cc_start: 0.7954 (t80) cc_final: 0.7341 (t80) REVERT: D 46 ARG cc_start: 0.6857 (tpm170) cc_final: 0.6108 (tpm170) REVERT: D 135 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8117 (tm-30) REVERT: D 196 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7482 (pp20) REVERT: E 60 GLN cc_start: 0.9061 (pt0) cc_final: 0.8835 (pp30) REVERT: E 65 LYS cc_start: 0.9136 (pttt) cc_final: 0.8685 (pttt) REVERT: F 1 MET cc_start: 0.8018 (mtm) cc_final: 0.6663 (ttp) REVERT: F 11 HIS cc_start: 0.9220 (t-90) cc_final: 0.8539 (t-90) REVERT: F 75 GLU cc_start: 0.9439 (pt0) cc_final: 0.9203 (pp20) REVERT: G 8 GLN cc_start: 0.8348 (pt0) cc_final: 0.7501 (pp30) REVERT: G 46 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8894 (mm) REVERT: G 143 MET cc_start: 0.7367 (mmt) cc_final: 0.6971 (mmt) REVERT: H 26 MET cc_start: 0.8073 (ppp) cc_final: 0.7694 (ppp) REVERT: H 94 VAL cc_start: 0.9563 (OUTLIER) cc_final: 0.9356 (m) REVERT: I 99 LYS cc_start: 0.9145 (ttpt) cc_final: 0.8644 (mttm) REVERT: I 106 ASP cc_start: 0.8498 (t70) cc_final: 0.8285 (t0) REVERT: I 122 ARG cc_start: 0.8187 (tpt90) cc_final: 0.7652 (mmm160) REVERT: J 24 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8758 (tt0) REVERT: J 42 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8018 (mm) REVERT: J 47 GLU cc_start: 0.8154 (mp0) cc_final: 0.7650 (mp0) REVERT: J 65 TYR cc_start: 0.6473 (m-80) cc_final: 0.4634 (m-80) REVERT: J 75 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: J 81 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8199 (mp0) REVERT: K 13 LYS cc_start: 0.8955 (tptp) cc_final: 0.8593 (mtmt) REVERT: K 112 VAL cc_start: 0.8700 (m) cc_final: 0.8020 (t) REVERT: L 23 LEU cc_start: 0.9000 (tp) cc_final: 0.8781 (tt) REVERT: M 90 HIS cc_start: 0.9107 (m-70) cc_final: 0.8499 (m170) REVERT: N 84 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8000 (ttm-80) REVERT: O 41 HIS cc_start: 0.7389 (t70) cc_final: 0.6762 (t70) REVERT: O 47 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7888 (pttm) REVERT: R 72 ARG cc_start: 0.6945 (tpp-160) cc_final: 0.5810 (tpp80) REVERT: S 65 MET cc_start: 0.8757 (mtm) cc_final: 0.8452 (ptp) REVERT: T 23 ARG cc_start: 0.9232 (mmm160) cc_final: 0.8846 (mpp80) REVERT: T 58 ASP cc_start: 0.8706 (t0) cc_final: 0.8409 (p0) REVERT: U 20 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6714 (pmm150) REVERT: U 30 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: U 53 LYS cc_start: 0.8488 (pttt) cc_final: 0.7565 (mmtt) REVERT: U 57 LYS cc_start: 0.8399 (mmpt) cc_final: 0.7530 (tmtt) REVERT: 03 53 ARG cc_start: 0.6761 (mpt180) cc_final: 0.6397 (mmt180) REVERT: 03 165 ASN cc_start: 0.6029 (OUTLIER) cc_final: 0.5819 (p0) REVERT: 03 218 MET cc_start: 0.7589 (mtp) cc_final: 0.6591 (mtp) REVERT: Z 13 ASN cc_start: 0.5821 (p0) cc_final: 0.5497 (p0) outliers start: 443 outliers final: 340 residues processed: 1033 average time/residue: 1.3248 time to fit residues: 2403.7684 Evaluate side-chains 1044 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 682 time to evaluate : 6.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 64 VAL Chi-restraints excluded: chain 04 residue 87 SER Chi-restraints excluded: chain 04 residue 97 ASP Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 132 ARG Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 202 ARG Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 266 ILE Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 51 THR Chi-restraints excluded: chain 05 residue 77 ARG Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 108 ASP Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 203 VAL Chi-restraints excluded: chain 06 residue 113 VAL Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 07 residue 3 LEU Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 20 ASN Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 90 LEU Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 07 residue 172 PHE Chi-restraints excluded: chain 07 residue 173 ASP Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 106 LEU Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 19 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 61 VAL Chi-restraints excluded: chain 09 residue 62 LEU Chi-restraints excluded: chain 09 residue 80 ILE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 147 VAL Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 19 ASP Chi-restraints excluded: chain 12 residue 45 THR Chi-restraints excluded: chain 12 residue 60 ASP Chi-restraints excluded: chain 12 residue 89 PHE Chi-restraints excluded: chain 12 residue 103 ILE Chi-restraints excluded: chain 12 residue 109 LEU Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 3 GLN Chi-restraints excluded: chain 13 residue 8 LEU Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 14 SER Chi-restraints excluded: chain 13 residue 22 ILE Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 95 ILE Chi-restraints excluded: chain 13 residue 108 ARG Chi-restraints excluded: chain 13 residue 109 SER Chi-restraints excluded: chain 13 residue 111 LYS Chi-restraints excluded: chain 13 residue 118 LEU Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 73 ILE Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 81 ASP Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 16 residue 29 VAL Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 38 LEU Chi-restraints excluded: chain 16 residue 75 ILE Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 16 residue 120 GLU Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 24 THR Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 94 ARG Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 4 ILE Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 32 VAL Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 80 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 96 LEU Chi-restraints excluded: chain 18 residue 98 TYR Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 39 ILE Chi-restraints excluded: chain 19 residue 43 GLN Chi-restraints excluded: chain 19 residue 46 TYR Chi-restraints excluded: chain 19 residue 75 TYR Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 99 VAL Chi-restraints excluded: chain 19 residue 110 GLU Chi-restraints excluded: chain 20 residue 13 ARG Chi-restraints excluded: chain 20 residue 15 SER Chi-restraints excluded: chain 20 residue 20 VAL Chi-restraints excluded: chain 20 residue 49 ILE Chi-restraints excluded: chain 20 residue 55 ASP Chi-restraints excluded: chain 20 residue 80 ARG Chi-restraints excluded: chain 20 residue 95 ASP Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 19 LEU Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 71 VAL Chi-restraints excluded: chain 22 residue 25 GLU Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 40 LEU Chi-restraints excluded: chain 23 residue 58 VAL Chi-restraints excluded: chain 23 residue 65 GLN Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 45 ASP Chi-restraints excluded: chain 24 residue 61 LEU Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 76 ILE Chi-restraints excluded: chain 26 residue 10 ARG Chi-restraints excluded: chain 26 residue 16 ASN Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 67 LEU Chi-restraints excluded: chain 26 residue 70 LEU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 16 LEU Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 4 ASP Chi-restraints excluded: chain 29 residue 21 VAL Chi-restraints excluded: chain 29 residue 22 MET Chi-restraints excluded: chain 29 residue 35 ASP Chi-restraints excluded: chain 29 residue 47 LYS Chi-restraints excluded: chain 29 residue 48 GLN Chi-restraints excluded: chain 29 residue 50 ASP Chi-restraints excluded: chain 29 residue 66 ILE Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 18 HIS Chi-restraints excluded: chain 30 residue 21 LEU Chi-restraints excluded: chain 30 residue 42 ILE Chi-restraints excluded: chain 31 residue 31 GLU Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 8 SER Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 56 LEU Chi-restraints excluded: chain 33 residue 58 ILE Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 GLN Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 84 ARG Chi-restraints excluded: chain N residue 100 TRP Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 71 SER Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 11 PHE Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 20 ARG Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 22 ASP Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 69 THR Chi-restraints excluded: chain 03 residue 165 ASN Chi-restraints excluded: chain 03 residue 178 VAL Chi-restraints excluded: chain 03 residue 192 LEU Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain 03 residue 225 ASP Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 65 SER Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 108 THR Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Z residue 320 THR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 656 optimal weight: 20.0000 chunk 423 optimal weight: 6.9990 chunk 633 optimal weight: 20.0000 chunk 319 optimal weight: 0.0470 chunk 208 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 674 optimal weight: 20.0000 chunk 722 optimal weight: 20.0000 chunk 524 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 834 optimal weight: 10.0000 overall best weight: 6.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 06 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 88 HIS ** 14 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 65 GLN 26 16 ASN 33 27 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN E 76 ASN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 HIS ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN ** Z 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 166780 Z= 0.219 Angle : 0.699 16.970 249021 Z= 0.359 Chirality : 0.038 0.343 31775 Planarity : 0.005 0.056 13713 Dihedral : 24.329 179.453 82263 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.14 % Favored : 87.56 % Rotamer: Outliers : 5.88 % Allowed : 25.98 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.10), residues: 6366 helix: -0.92 (0.11), residues: 1934 sheet: -2.24 (0.15), residues: 987 loop : -2.60 (0.10), residues: 3445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 17 HIS 0.011 0.001 HIS D 197 PHE 0.026 0.002 PHE27 26 TYR 0.025 0.002 TYR B 212 ARG 0.011 0.001 ARG08 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 808 time to evaluate : 6.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 05 11 MET cc_start: 0.6762 (tpt) cc_final: 0.6296 (tpt) REVERT: 05 42 ASN cc_start: 0.8932 (m110) cc_final: 0.8121 (t0) REVERT: 05 90 PHE cc_start: 0.7958 (m-80) cc_final: 0.7673 (m-10) REVERT: 05 148 GLN cc_start: 0.8345 (mp10) cc_final: 0.7977 (mt0) REVERT: 06 100 MET cc_start: 0.8875 (mtt) cc_final: 0.8246 (mmt) REVERT: 06 153 LEU cc_start: 0.7658 (tp) cc_final: 0.6939 (mt) REVERT: 06 176 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8298 (p0) REVERT: 07 9 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.6996 (p0) REVERT: 07 82 TYR cc_start: 0.8671 (t80) cc_final: 0.8179 (t80) REVERT: 07 89 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7731 (p) REVERT: 08 175 LYS cc_start: 0.4629 (tttt) cc_final: 0.4013 (tptt) REVERT: 09 12 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8348 (pp) REVERT: 10 52 MET cc_start: 0.1582 (ttp) cc_final: 0.0791 (mtt) REVERT: 10 86 MET cc_start: -0.0554 (mmt) cc_final: -0.1352 (mmt) REVERT: 10 99 PHE cc_start: 0.7444 (m-10) cc_final: 0.6935 (m-10) REVERT: 10 122 GLN cc_start: 0.8206 (pm20) cc_final: 0.7813 (pp30) REVERT: 11 64 ARG cc_start: 0.7485 (tpt-90) cc_final: 0.7047 (mmp80) REVERT: 11 102 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8271 (ttp80) REVERT: 11 116 MET cc_start: 0.2772 (mmp) cc_final: 0.1228 (tpp) REVERT: 11 135 MET cc_start: 0.4369 (tpp) cc_final: 0.3809 (tpp) REVERT: 13 49 ARG cc_start: 0.8440 (mmp-170) cc_final: 0.8148 (mmp-170) REVERT: 13 93 GLN cc_start: 0.8395 (mp10) cc_final: 0.8085 (mp10) REVERT: 13 108 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7284 (ptm-80) REVERT: 13 111 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8089 (ptpp) REVERT: 13 121 GLU cc_start: 0.7996 (pt0) cc_final: 0.7689 (pm20) REVERT: 14 51 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8397 (mp0) REVERT: 14 77 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8309 (tp) REVERT: 14 115 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6602 (tm-30) REVERT: 15 53 MET cc_start: 0.8543 (mmm) cc_final: 0.8263 (mpp) REVERT: 15 60 GLN cc_start: 0.8507 (pp30) cc_final: 0.8070 (pp30) REVERT: 16 18 GLN cc_start: 0.9055 (tt0) cc_final: 0.8147 (tm-30) REVERT: 16 20 MET cc_start: 0.8681 (ppp) cc_final: 0.8397 (ppp) REVERT: 17 94 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7971 (ttp-170) REVERT: 18 12 MET cc_start: 0.8580 (ttp) cc_final: 0.8272 (ttm) REVERT: 20 13 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8076 (ttt90) REVERT: 20 80 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7900 (ptp-110) REVERT: 20 82 HIS cc_start: 0.8325 (t-90) cc_final: 0.7962 (t-170) REVERT: 21 31 GLN cc_start: 0.9282 (mt0) cc_final: 0.9015 (pp30) REVERT: 21 52 GLU cc_start: 0.8237 (pt0) cc_final: 0.7898 (pp20) REVERT: 22 1 MET cc_start: 0.5657 (mtt) cc_final: 0.5384 (mtt) REVERT: 22 42 GLU cc_start: 0.8779 (mp0) cc_final: 0.8556 (mp0) REVERT: 22 52 GLU cc_start: 0.9199 (tt0) cc_final: 0.8882 (tp30) REVERT: 23 17 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.7950 (t0) REVERT: 23 18 LYS cc_start: 0.9635 (tmmt) cc_final: 0.9378 (ttmt) REVERT: 24 45 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8463 (t0) REVERT: 25 40 LYS cc_start: 0.8727 (mttt) cc_final: 0.7803 (mttp) REVERT: 25 64 LYS cc_start: 0.9037 (tppp) cc_final: 0.8698 (tppt) REVERT: 26 37 PHE cc_start: 0.9099 (m-80) cc_final: 0.8730 (m-80) REVERT: 26 39 VAL cc_start: 0.8932 (t) cc_final: 0.8658 (p) REVERT: 26 69 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8604 (mt-10) REVERT: 27 59 GLU cc_start: 0.9448 (tt0) cc_final: 0.9110 (mt-10) REVERT: 28 46 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8519 (tpp) REVERT: 29 1 MET cc_start: 0.7497 (mtt) cc_final: 0.7134 (tmm) REVERT: 30 27 LEU cc_start: 0.8850 (mp) cc_final: 0.8502 (mt) REVERT: 31 37 LYS cc_start: 0.8588 (mttm) cc_final: 0.8261 (mmtp) REVERT: 32 8 SER cc_start: 0.8482 (OUTLIER) cc_final: 0.7996 (p) REVERT: 34 2 LYS cc_start: 0.7000 (mmtt) cc_final: 0.6617 (mmtp) REVERT: B 93 HIS cc_start: 0.8520 (m170) cc_final: 0.7907 (m-70) REVERT: B 94 ARG cc_start: 0.7824 (mpt180) cc_final: 0.6884 (tpt170) REVERT: C 17 TRP cc_start: 0.7949 (m-10) cc_final: 0.7671 (m-10) REVERT: C 128 MET cc_start: 0.8181 (tpt) cc_final: 0.7854 (tpt) REVERT: C 180 ASP cc_start: 0.9005 (t70) cc_final: 0.8631 (p0) REVERT: C 182 ASP cc_start: 0.8646 (t0) cc_final: 0.8225 (p0) REVERT: D 3 TYR cc_start: 0.7899 (t80) cc_final: 0.7323 (t80) REVERT: D 46 ARG cc_start: 0.6888 (tpm170) cc_final: 0.6117 (tpm170) REVERT: D 47 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7760 (pp) REVERT: D 135 GLN cc_start: 0.8478 (tm-30) cc_final: 0.7920 (tm-30) REVERT: D 196 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7444 (pp20) REVERT: E 60 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8767 (pp30) REVERT: E 65 LYS cc_start: 0.9083 (pttt) cc_final: 0.8696 (pttt) REVERT: E 144 GLU cc_start: 0.8952 (tp30) cc_final: 0.8632 (tp30) REVERT: F 11 HIS cc_start: 0.9215 (t-90) cc_final: 0.8535 (t-90) REVERT: F 75 GLU cc_start: 0.9403 (pt0) cc_final: 0.9087 (pp20) REVERT: G 8 GLN cc_start: 0.8333 (pt0) cc_final: 0.7556 (pp30) REVERT: G 46 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8865 (mm) REVERT: G 143 MET cc_start: 0.7250 (mmt) cc_final: 0.6854 (mmt) REVERT: H 26 MET cc_start: 0.7731 (ppp) cc_final: 0.7377 (ppp) REVERT: I 29 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7947 (pt) REVERT: I 93 LEU cc_start: 0.9278 (mt) cc_final: 0.8995 (pp) REVERT: I 106 ASP cc_start: 0.8526 (t70) cc_final: 0.8315 (t0) REVERT: I 117 LEU cc_start: 0.9102 (mm) cc_final: 0.8493 (tp) REVERT: I 122 ARG cc_start: 0.8260 (tpt90) cc_final: 0.7709 (tpt-90) REVERT: J 42 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7778 (mm) REVERT: J 75 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.6982 (m-30) REVERT: J 81 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8239 (mp0) REVERT: K 13 LYS cc_start: 0.8937 (tptp) cc_final: 0.8596 (mtmt) REVERT: K 124 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6906 (pttm) REVERT: M 90 HIS cc_start: 0.8980 (m-70) cc_final: 0.8408 (m170) REVERT: M 91 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7650 (mtm180) REVERT: M 92 ARG cc_start: 0.9217 (mtp85) cc_final: 0.8678 (mpt180) REVERT: N 17 ASP cc_start: 0.9020 (m-30) cc_final: 0.8450 (p0) REVERT: O 10 ILE cc_start: 0.9206 (mt) cc_final: 0.8977 (tt) REVERT: O 32 THR cc_start: 0.9227 (m) cc_final: 0.8969 (p) REVERT: O 41 HIS cc_start: 0.7569 (t70) cc_final: 0.6806 (t70) REVERT: O 47 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7774 (pttm) REVERT: Q 35 LYS cc_start: 0.9174 (tptp) cc_final: 0.8849 (tptt) REVERT: S 65 MET cc_start: 0.8737 (mtm) cc_final: 0.8249 (ptp) REVERT: T 27 MET cc_start: 0.9459 (mmm) cc_final: 0.8972 (mmm) REVERT: U 20 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6947 (mtm-85) REVERT: U 53 LYS cc_start: 0.8577 (pttt) cc_final: 0.7735 (mmtt) REVERT: U 57 LYS cc_start: 0.8408 (mmpt) cc_final: 0.7604 (tmtt) REVERT: 03 53 ARG cc_start: 0.6629 (mpt180) cc_final: 0.6301 (mmt180) REVERT: 03 165 ASN cc_start: 0.5995 (OUTLIER) cc_final: 0.5720 (p0) REVERT: 03 218 MET cc_start: 0.7506 (mtp) cc_final: 0.6478 (mtp) REVERT: Z 13 ASN cc_start: 0.6158 (p0) cc_final: 0.5764 (p0) REVERT: Z 155 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7500 (tm-30) REVERT: Z 159 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6660 (tt0) outliers start: 311 outliers final: 234 residues processed: 1018 average time/residue: 1.3168 time to fit residues: 2350.0568 Evaluate side-chains 1009 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 748 time to evaluate : 6.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 53 ILE Chi-restraints excluded: chain 04 residue 87 SER Chi-restraints excluded: chain 04 residue 97 ASP Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 132 ARG Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 266 ILE Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 77 ARG Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 108 ASP Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 203 VAL Chi-restraints excluded: chain 06 residue 113 VAL Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 06 residue 176 ASP Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 90 LEU Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 07 residue 173 ASP Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 106 LEU Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 19 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 80 ILE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 19 ASP Chi-restraints excluded: chain 12 residue 60 ASP Chi-restraints excluded: chain 12 residue 109 LEU Chi-restraints excluded: chain 13 residue 3 GLN Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 95 ILE Chi-restraints excluded: chain 13 residue 108 ARG Chi-restraints excluded: chain 13 residue 109 SER Chi-restraints excluded: chain 13 residue 111 LYS Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 81 ASP Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 24 THR Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 94 ARG Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 4 ILE Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 32 VAL Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 80 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 39 ILE Chi-restraints excluded: chain 19 residue 43 GLN Chi-restraints excluded: chain 19 residue 46 TYR Chi-restraints excluded: chain 19 residue 75 TYR Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 99 VAL Chi-restraints excluded: chain 20 residue 13 ARG Chi-restraints excluded: chain 20 residue 15 SER Chi-restraints excluded: chain 20 residue 20 VAL Chi-restraints excluded: chain 20 residue 80 ARG Chi-restraints excluded: chain 20 residue 95 ASP Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 71 VAL Chi-restraints excluded: chain 22 residue 25 GLU Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 40 LEU Chi-restraints excluded: chain 23 residue 58 VAL Chi-restraints excluded: chain 23 residue 65 GLN Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 45 ASP Chi-restraints excluded: chain 24 residue 61 LEU Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 75 PHE Chi-restraints excluded: chain 25 residue 76 ILE Chi-restraints excluded: chain 26 residue 10 ARG Chi-restraints excluded: chain 26 residue 16 ASN Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 67 LEU Chi-restraints excluded: chain 26 residue 70 LEU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 16 LEU Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 46 MET Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 35 ASP Chi-restraints excluded: chain 29 residue 48 GLN Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 21 LEU Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 31 GLU Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 32 residue 8 SER Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 4 LYS Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 84 ARG Chi-restraints excluded: chain N residue 100 TRP Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 71 SER Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain U residue 11 PHE Chi-restraints excluded: chain U residue 20 ARG Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 69 THR Chi-restraints excluded: chain 03 residue 165 ASN Chi-restraints excluded: chain 03 residue 178 VAL Chi-restraints excluded: chain 03 residue 180 PHE Chi-restraints excluded: chain 03 residue 192 LEU Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 65 SER Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 108 THR Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 159 GLN Chi-restraints excluded: chain Z residue 251 GLN Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Z residue 320 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 965 optimal weight: 30.0000 chunk 1016 optimal weight: 30.0000 chunk 927 optimal weight: 30.0000 chunk 988 optimal weight: 30.0000 chunk 595 optimal weight: 30.0000 chunk 430 optimal weight: 8.9990 chunk 776 optimal weight: 20.0000 chunk 303 optimal weight: 20.0000 chunk 893 optimal weight: 20.0000 chunk 935 optimal weight: 20.0000 chunk 985 optimal weight: 20.0000 overall best weight: 17.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 06 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 126 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 26 16 ASN 28 48 ASN 33 27 ASN ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.133 166780 Z= 0.470 Angle : 0.897 19.095 249021 Z= 0.454 Chirality : 0.047 0.390 31775 Planarity : 0.007 0.069 13713 Dihedral : 24.524 178.557 82263 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 43.14 Ramachandran Plot: Outliers : 0.35 % Allowed : 15.82 % Favored : 83.84 % Rotamer: Outliers : 6.68 % Allowed : 25.49 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.10), residues: 6366 helix: -1.28 (0.11), residues: 1939 sheet: -2.27 (0.15), residues: 965 loop : -2.83 (0.10), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 17 HIS 0.033 0.003 HIS O 45 PHE 0.038 0.003 PHE15 117 TYR 0.026 0.003 TYR O 77 ARG 0.013 0.001 ARG21 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 701 time to evaluate : 6.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 05 42 ASN cc_start: 0.8947 (m110) cc_final: 0.8117 (t0) REVERT: 05 90 PHE cc_start: 0.8126 (m-80) cc_final: 0.7816 (m-10) REVERT: 05 148 GLN cc_start: 0.8558 (mp10) cc_final: 0.8120 (mt0) REVERT: 06 153 LEU cc_start: 0.7558 (tp) cc_final: 0.6720 (mt) REVERT: 07 82 TYR cc_start: 0.8824 (t80) cc_final: 0.8488 (t80) REVERT: 08 175 LYS cc_start: 0.4720 (tttt) cc_final: 0.3995 (tptt) REVERT: 09 12 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8419 (pp) REVERT: 10 52 MET cc_start: 0.2154 (ttp) cc_final: 0.1395 (mtt) REVERT: 10 86 MET cc_start: -0.0217 (mmt) cc_final: -0.0949 (mmt) REVERT: 10 99 PHE cc_start: 0.7481 (m-10) cc_final: 0.6965 (m-10) REVERT: 11 116 MET cc_start: 0.3028 (mmp) cc_final: 0.1252 (tpp) REVERT: 11 135 MET cc_start: 0.4384 (tpp) cc_final: 0.3981 (tpp) REVERT: 13 49 ARG cc_start: 0.8467 (mmp-170) cc_final: 0.8139 (mmp-170) REVERT: 13 93 GLN cc_start: 0.8463 (mp10) cc_final: 0.8123 (mp10) REVERT: 13 111 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8029 (ptpp) REVERT: 14 51 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8162 (mp0) REVERT: 14 77 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8455 (tp) REVERT: 14 115 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6707 (tm-30) REVERT: 14 144 GLU cc_start: 0.7030 (pt0) cc_final: 0.6536 (mm-30) REVERT: 15 136 MET cc_start: 0.8114 (tpp) cc_final: 0.7648 (tpp) REVERT: 16 18 GLN cc_start: 0.9105 (tt0) cc_final: 0.8220 (tm-30) REVERT: 17 5 SER cc_start: 0.9029 (t) cc_final: 0.8623 (m) REVERT: 17 94 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8040 (ttp-170) REVERT: 18 12 MET cc_start: 0.8635 (ttp) cc_final: 0.8306 (ttm) REVERT: 19 43 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.9113 (pm20) REVERT: 20 13 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8146 (ttt90) REVERT: 20 40 MET cc_start: 0.9223 (tpp) cc_final: 0.8991 (tpp) REVERT: 20 80 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8101 (ptp-110) REVERT: 20 82 HIS cc_start: 0.8375 (t-90) cc_final: 0.8006 (t-170) REVERT: 21 31 GLN cc_start: 0.9350 (mt0) cc_final: 0.8966 (pp30) REVERT: 21 52 GLU cc_start: 0.8238 (pt0) cc_final: 0.7940 (pp20) REVERT: 22 1 MET cc_start: 0.6222 (mtt) cc_final: 0.5504 (mtm) REVERT: 23 18 LYS cc_start: 0.9630 (tmmt) cc_final: 0.9380 (ttmt) REVERT: 25 40 LYS cc_start: 0.8771 (mttt) cc_final: 0.7870 (mtmm) REVERT: 25 64 LYS cc_start: 0.9036 (tppp) cc_final: 0.8803 (tppt) REVERT: 26 69 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8699 (mt-10) REVERT: 27 20 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8742 (p0) REVERT: 27 59 GLU cc_start: 0.9471 (tt0) cc_final: 0.9139 (mt-10) REVERT: 28 18 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8404 (mmtt) REVERT: 28 46 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8603 (tpp) REVERT: 30 27 LEU cc_start: 0.9011 (mp) cc_final: 0.8753 (mt) REVERT: 34 2 LYS cc_start: 0.7264 (mmtt) cc_final: 0.6883 (mmtp) REVERT: B 93 HIS cc_start: 0.8541 (m170) cc_final: 0.7909 (m-70) REVERT: B 94 ARG cc_start: 0.8005 (mpt180) cc_final: 0.7046 (tpt170) REVERT: C 17 TRP cc_start: 0.8050 (m-10) cc_final: 0.7736 (m-10) REVERT: C 128 MET cc_start: 0.8193 (tpt) cc_final: 0.7928 (tpp) REVERT: C 169 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8370 (tm-30) REVERT: C 180 ASP cc_start: 0.9000 (t70) cc_final: 0.8427 (p0) REVERT: C 182 ASP cc_start: 0.8715 (t0) cc_final: 0.8186 (p0) REVERT: D 3 TYR cc_start: 0.7882 (t80) cc_final: 0.7288 (t80) REVERT: D 46 ARG cc_start: 0.6877 (tpm170) cc_final: 0.6107 (tpm170) REVERT: D 135 GLN cc_start: 0.8488 (tm-30) cc_final: 0.7933 (tm-30) REVERT: D 196 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7476 (pp20) REVERT: E 60 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8823 (pp30) REVERT: E 65 LYS cc_start: 0.9136 (pttt) cc_final: 0.8717 (pttt) REVERT: F 1 MET cc_start: 0.7907 (mtm) cc_final: 0.6904 (ttp) REVERT: F 11 HIS cc_start: 0.9192 (t-90) cc_final: 0.8502 (t-90) REVERT: F 75 GLU cc_start: 0.9432 (pt0) cc_final: 0.9175 (pp20) REVERT: G 8 GLN cc_start: 0.8363 (pt0) cc_final: 0.7531 (pp30) REVERT: G 46 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8890 (mm) REVERT: H 26 MET cc_start: 0.7865 (ppp) cc_final: 0.7466 (ppp) REVERT: I 99 LYS cc_start: 0.9148 (ttpt) cc_final: 0.8624 (mttm) REVERT: I 106 ASP cc_start: 0.8498 (t70) cc_final: 0.8282 (t0) REVERT: I 117 LEU cc_start: 0.9045 (mm) cc_final: 0.8302 (tp) REVERT: I 122 ARG cc_start: 0.8083 (tpt90) cc_final: 0.7545 (mmm160) REVERT: J 42 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7977 (mm) REVERT: J 75 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7056 (m-30) REVERT: J 81 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8189 (mp0) REVERT: K 13 LYS cc_start: 0.8986 (tptp) cc_final: 0.8639 (mtmt) REVERT: K 124 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7131 (pttm) REVERT: M 90 HIS cc_start: 0.9060 (m-70) cc_final: 0.8461 (m170) REVERT: N 84 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8021 (ttm-80) REVERT: O 10 ILE cc_start: 0.9295 (mt) cc_final: 0.9065 (tt) REVERT: O 41 HIS cc_start: 0.7459 (t70) cc_final: 0.6835 (t70) REVERT: O 47 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7825 (pttm) REVERT: Q 35 LYS cc_start: 0.9210 (tptp) cc_final: 0.8861 (tptt) REVERT: Q 36 PHE cc_start: 0.7888 (m-80) cc_final: 0.7480 (t80) REVERT: S 65 MET cc_start: 0.8800 (mtm) cc_final: 0.8433 (ptp) REVERT: T 58 ASP cc_start: 0.8575 (t0) cc_final: 0.8309 (p0) REVERT: U 20 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6106 (mtm-85) REVERT: U 30 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: U 53 LYS cc_start: 0.8610 (pttt) cc_final: 0.7747 (mmtt) REVERT: U 57 LYS cc_start: 0.8359 (mmpt) cc_final: 0.7479 (tmtt) REVERT: 03 53 ARG cc_start: 0.6823 (mpt180) cc_final: 0.6470 (mmt180) REVERT: 03 165 ASN cc_start: 0.5998 (OUTLIER) cc_final: 0.5742 (p0) REVERT: 03 218 MET cc_start: 0.7649 (mtp) cc_final: 0.6669 (mtp) REVERT: Z 13 ASN cc_start: 0.6003 (p0) cc_final: 0.5596 (p0) outliers start: 353 outliers final: 298 residues processed: 953 average time/residue: 1.3216 time to fit residues: 2214.5329 Evaluate side-chains 1008 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 689 time to evaluate : 6.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 82 TYR Chi-restraints excluded: chain 04 residue 87 SER Chi-restraints excluded: chain 04 residue 97 ASP Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 132 ARG Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 266 ILE Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 77 ARG Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 108 ASP Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 203 VAL Chi-restraints excluded: chain 06 residue 113 VAL Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 20 ASN Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 90 LEU Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 07 residue 172 PHE Chi-restraints excluded: chain 07 residue 173 ASP Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 106 LEU Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 19 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 61 VAL Chi-restraints excluded: chain 09 residue 80 ILE Chi-restraints excluded: chain 09 residue 147 VAL Chi-restraints excluded: chain 10 residue 7 ASP Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 111 THR Chi-restraints excluded: chain 11 residue 137 LEU Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 19 ASP Chi-restraints excluded: chain 12 residue 60 ASP Chi-restraints excluded: chain 12 residue 89 PHE Chi-restraints excluded: chain 12 residue 109 LEU Chi-restraints excluded: chain 13 residue 3 GLN Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 95 ILE Chi-restraints excluded: chain 13 residue 108 ARG Chi-restraints excluded: chain 13 residue 109 SER Chi-restraints excluded: chain 13 residue 111 LYS Chi-restraints excluded: chain 13 residue 118 LEU Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 33 ARG Chi-restraints excluded: chain 14 residue 73 ILE Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 81 ASP Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 14 residue 143 GLU Chi-restraints excluded: chain 15 residue 1 MET Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 29 VAL Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 38 LEU Chi-restraints excluded: chain 16 residue 119 SER Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 24 THR Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 17 residue 94 ARG Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 4 ILE Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 32 VAL Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 80 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 39 ILE Chi-restraints excluded: chain 19 residue 43 GLN Chi-restraints excluded: chain 19 residue 46 TYR Chi-restraints excluded: chain 19 residue 75 TYR Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 93 ILE Chi-restraints excluded: chain 19 residue 96 ASP Chi-restraints excluded: chain 20 residue 13 ARG Chi-restraints excluded: chain 20 residue 15 SER Chi-restraints excluded: chain 20 residue 20 VAL Chi-restraints excluded: chain 20 residue 49 ILE Chi-restraints excluded: chain 20 residue 55 ASP Chi-restraints excluded: chain 20 residue 80 ARG Chi-restraints excluded: chain 20 residue 95 ASP Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 71 VAL Chi-restraints excluded: chain 22 residue 25 GLU Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 40 LEU Chi-restraints excluded: chain 23 residue 58 VAL Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 45 ASP Chi-restraints excluded: chain 24 residue 61 LEU Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 75 PHE Chi-restraints excluded: chain 25 residue 76 ILE Chi-restraints excluded: chain 26 residue 10 ARG Chi-restraints excluded: chain 26 residue 16 ASN Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 67 LEU Chi-restraints excluded: chain 26 residue 70 LEU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 20 ASN Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 46 MET Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 4 ASP Chi-restraints excluded: chain 29 residue 21 VAL Chi-restraints excluded: chain 29 residue 22 MET Chi-restraints excluded: chain 29 residue 35 ASP Chi-restraints excluded: chain 29 residue 47 LYS Chi-restraints excluded: chain 29 residue 48 GLN Chi-restraints excluded: chain 29 residue 66 ILE Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 21 LEU Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 31 GLU Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 32 residue 8 SER Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 58 ILE Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 4 ARG Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 GLN Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 84 ARG Chi-restraints excluded: chain N residue 100 TRP Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 71 SER Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 11 PHE Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 20 ARG Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 69 THR Chi-restraints excluded: chain 03 residue 165 ASN Chi-restraints excluded: chain 03 residue 178 VAL Chi-restraints excluded: chain 03 residue 180 PHE Chi-restraints excluded: chain 03 residue 192 LEU Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain 03 residue 225 ASP Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 65 SER Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 108 THR Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 159 GLN Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Z residue 320 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 649 optimal weight: 20.0000 chunk 1045 optimal weight: 50.0000 chunk 638 optimal weight: 30.0000 chunk 496 optimal weight: 6.9990 chunk 726 optimal weight: 20.0000 chunk 1096 optimal weight: 6.9990 chunk 1009 optimal weight: 20.0000 chunk 873 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 674 optimal weight: 20.0000 chunk 535 optimal weight: 0.0870 overall best weight: 8.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 06 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 126 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN E 76 ASN E 96 GLN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 66 HIS Z 251 GLN ** Z 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 166780 Z= 0.246 Angle : 0.715 16.874 249021 Z= 0.367 Chirality : 0.039 0.406 31775 Planarity : 0.005 0.117 13713 Dihedral : 24.393 178.605 82263 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 30.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.65 % Favored : 87.06 % Rotamer: Outliers : 5.60 % Allowed : 26.64 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.10), residues: 6366 helix: -0.89 (0.11), residues: 1915 sheet: -2.17 (0.16), residues: 968 loop : -2.60 (0.10), residues: 3483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 17 HIS 0.020 0.002 HIS O 45 PHE 0.046 0.002 PHE15 117 TYR 0.027 0.002 TYR O 77 ARG 0.033 0.001 ARG08 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 749 time to evaluate : 6.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 05 11 MET cc_start: 0.6817 (tpt) cc_final: 0.6318 (tpt) REVERT: 05 42 ASN cc_start: 0.8948 (m110) cc_final: 0.8134 (t0) REVERT: 05 90 PHE cc_start: 0.7973 (m-80) cc_final: 0.7700 (m-10) REVERT: 05 148 GLN cc_start: 0.8414 (mp10) cc_final: 0.8041 (mt0) REVERT: 06 100 MET cc_start: 0.8898 (mtt) cc_final: 0.8283 (mmt) REVERT: 06 153 LEU cc_start: 0.7590 (tp) cc_final: 0.6848 (mt) REVERT: 07 82 TYR cc_start: 0.8692 (t80) cc_final: 0.8151 (t80) REVERT: 07 89 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7723 (p) REVERT: 08 175 LYS cc_start: 0.4643 (tttt) cc_final: 0.3949 (tptt) REVERT: 10 52 MET cc_start: 0.2325 (ttp) cc_final: 0.1463 (mtt) REVERT: 10 86 MET cc_start: -0.0078 (mmt) cc_final: -0.1058 (mmt) REVERT: 10 99 PHE cc_start: 0.7511 (m-10) cc_final: 0.6970 (m-10) REVERT: 11 64 ARG cc_start: 0.7491 (tpt-90) cc_final: 0.7013 (mmp80) REVERT: 11 102 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8252 (ttp80) REVERT: 11 116 MET cc_start: 0.2929 (mmp) cc_final: 0.1206 (tpp) REVERT: 11 135 MET cc_start: 0.4041 (tpp) cc_final: 0.3577 (tpp) REVERT: 13 49 ARG cc_start: 0.8435 (mmp-170) cc_final: 0.8127 (mmp-170) REVERT: 13 93 GLN cc_start: 0.8455 (mp10) cc_final: 0.8113 (mp10) REVERT: 13 111 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8109 (ptpp) REVERT: 13 121 GLU cc_start: 0.8042 (pt0) cc_final: 0.7714 (pm20) REVERT: 14 51 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8451 (mp0) REVERT: 14 77 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8328 (tp) REVERT: 14 115 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6676 (tm-30) REVERT: 15 60 GLN cc_start: 0.8500 (pp30) cc_final: 0.8088 (pp30) REVERT: 15 136 MET cc_start: 0.7864 (tpp) cc_final: 0.7451 (tpp) REVERT: 16 18 GLN cc_start: 0.9049 (tt0) cc_final: 0.8156 (tm-30) REVERT: 16 20 MET cc_start: 0.8703 (ppp) cc_final: 0.8421 (ppp) REVERT: 17 5 SER cc_start: 0.8953 (t) cc_final: 0.8546 (m) REVERT: 17 94 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7985 (ttp-170) REVERT: 18 12 MET cc_start: 0.8573 (ttp) cc_final: 0.8333 (ttm) REVERT: 20 13 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8088 (ttt90) REVERT: 20 40 MET cc_start: 0.9212 (tpp) cc_final: 0.8999 (tpp) REVERT: 20 76 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8795 (mmtt) REVERT: 20 80 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7895 (ptp-110) REVERT: 20 82 HIS cc_start: 0.8304 (t-90) cc_final: 0.7979 (t70) REVERT: 21 1 MET cc_start: 0.8642 (tmm) cc_final: 0.7581 (tmm) REVERT: 21 31 GLN cc_start: 0.9311 (mt0) cc_final: 0.9009 (pp30) REVERT: 21 52 GLU cc_start: 0.8233 (pt0) cc_final: 0.7925 (pp20) REVERT: 21 110 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.6322 (ptt90) REVERT: 22 1 MET cc_start: 0.5784 (mtt) cc_final: 0.5494 (mtt) REVERT: 22 42 GLU cc_start: 0.8845 (mp0) cc_final: 0.8636 (mp0) REVERT: 23 18 LYS cc_start: 0.9644 (tmmt) cc_final: 0.9382 (ttmt) REVERT: 25 40 LYS cc_start: 0.8727 (mttt) cc_final: 0.7827 (mttp) REVERT: 25 64 LYS cc_start: 0.9026 (tppp) cc_final: 0.8786 (tppt) REVERT: 26 37 PHE cc_start: 0.9105 (m-80) cc_final: 0.8750 (m-80) REVERT: 26 69 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8600 (mt-10) REVERT: 27 59 GLU cc_start: 0.9463 (tt0) cc_final: 0.9114 (mt-10) REVERT: 28 18 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8357 (mmtt) REVERT: 29 1 MET cc_start: 0.7579 (mtt) cc_final: 0.7181 (tmm) REVERT: 30 27 LEU cc_start: 0.8902 (mp) cc_final: 0.8534 (mt) REVERT: 32 8 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.7959 (p) REVERT: 34 2 LYS cc_start: 0.7129 (mmtt) cc_final: 0.6731 (mmtp) REVERT: B 55 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8942 (mp0) REVERT: B 93 HIS cc_start: 0.8515 (m170) cc_final: 0.7877 (m-70) REVERT: B 94 ARG cc_start: 0.7859 (mpt180) cc_final: 0.6912 (tpt170) REVERT: B 135 MET cc_start: 0.9325 (ptp) cc_final: 0.9042 (pmm) REVERT: B 189 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.6514 (t0) REVERT: C 17 TRP cc_start: 0.7954 (m-10) cc_final: 0.7629 (m-10) REVERT: C 128 MET cc_start: 0.8161 (tpt) cc_final: 0.7841 (tpt) REVERT: C 180 ASP cc_start: 0.8981 (t70) cc_final: 0.8622 (p0) REVERT: C 182 ASP cc_start: 0.8620 (t0) cc_final: 0.8175 (p0) REVERT: D 3 TYR cc_start: 0.7892 (t80) cc_final: 0.7349 (t80) REVERT: D 46 ARG cc_start: 0.6932 (tpm170) cc_final: 0.6109 (tpm170) REVERT: D 47 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7796 (pp) REVERT: D 135 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 196 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7478 (pp20) REVERT: E 60 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8793 (pp30) REVERT: E 65 LYS cc_start: 0.9098 (pttt) cc_final: 0.8661 (pttt) REVERT: E 144 GLU cc_start: 0.8885 (tp30) cc_final: 0.8561 (tp30) REVERT: F 11 HIS cc_start: 0.9218 (t-90) cc_final: 0.8479 (t-90) REVERT: F 75 GLU cc_start: 0.9404 (pt0) cc_final: 0.9111 (pp20) REVERT: F 85 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8435 (tt) REVERT: G 8 GLN cc_start: 0.8327 (pt0) cc_final: 0.7538 (pp30) REVERT: G 46 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8867 (mm) REVERT: H 26 MET cc_start: 0.7694 (ppp) cc_final: 0.7288 (ppp) REVERT: I 29 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7960 (pt) REVERT: I 93 LEU cc_start: 0.9338 (mt) cc_final: 0.9047 (pp) REVERT: I 106 ASP cc_start: 0.8496 (t70) cc_final: 0.8285 (t0) REVERT: I 117 LEU cc_start: 0.9128 (mm) cc_final: 0.8525 (tp) REVERT: J 42 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7793 (mm) REVERT: J 75 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.6970 (m-30) REVERT: J 81 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8211 (mp0) REVERT: K 13 LYS cc_start: 0.8978 (tptp) cc_final: 0.8631 (mtmt) REVERT: K 124 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6997 (pttm) REVERT: M 90 HIS cc_start: 0.8980 (m-70) cc_final: 0.8426 (m170) REVERT: M 91 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7270 (mtm180) REVERT: M 92 ARG cc_start: 0.9210 (mtp85) cc_final: 0.8806 (mpt180) REVERT: N 84 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.7955 (ttm-80) REVERT: O 10 ILE cc_start: 0.9207 (mt) cc_final: 0.8979 (tt) REVERT: O 32 THR cc_start: 0.9250 (m) cc_final: 0.8994 (p) REVERT: O 41 HIS cc_start: 0.7517 (t70) cc_final: 0.6880 (t70) REVERT: O 47 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7742 (pttm) REVERT: Q 36 PHE cc_start: 0.7767 (m-80) cc_final: 0.7093 (t80) REVERT: S 65 MET cc_start: 0.8717 (mtm) cc_final: 0.8025 (ptp) REVERT: U 20 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6947 (mtm-85) REVERT: U 30 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8333 (tm-30) REVERT: U 53 LYS cc_start: 0.8619 (pttt) cc_final: 0.7837 (mmtt) REVERT: U 57 LYS cc_start: 0.8369 (mmpt) cc_final: 0.7541 (tmtt) REVERT: 03 53 ARG cc_start: 0.6689 (mpt180) cc_final: 0.6363 (mmt180) REVERT: 03 218 MET cc_start: 0.7667 (mtp) cc_final: 0.6696 (mtp) REVERT: Z 13 ASN cc_start: 0.6141 (p0) cc_final: 0.5707 (p0) REVERT: Z 155 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7417 (tm-30) REVERT: Z 159 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6637 (tt0) outliers start: 296 outliers final: 243 residues processed: 963 average time/residue: 1.3338 time to fit residues: 2253.5799 Evaluate side-chains 996 residues out of total 5286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 729 time to evaluate : 6.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 53 ILE Chi-restraints excluded: chain 04 residue 87 SER Chi-restraints excluded: chain 04 residue 97 ASP Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 132 ARG Chi-restraints excluded: chain 04 residue 136 VAL Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 266 ILE Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 77 ARG Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 203 VAL Chi-restraints excluded: chain 06 residue 113 VAL Chi-restraints excluded: chain 06 residue 126 VAL Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 07 residue 3 LEU Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 20 ASN Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 90 LEU Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 07 residue 173 ASP Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 106 LEU Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 19 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 62 LEU Chi-restraints excluded: chain 09 residue 80 ILE Chi-restraints excluded: chain 10 residue 7 ASP Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 19 ASP Chi-restraints excluded: chain 12 residue 60 ASP Chi-restraints excluded: chain 12 residue 109 LEU Chi-restraints excluded: chain 13 residue 3 GLN Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 14 SER Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 95 ILE Chi-restraints excluded: chain 13 residue 109 SER Chi-restraints excluded: chain 13 residue 111 LYS Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 33 ARG Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 81 ASP Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 24 THR Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 17 residue 94 ARG Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 4 ILE Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 32 VAL Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 80 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 39 ILE Chi-restraints excluded: chain 19 residue 43 GLN Chi-restraints excluded: chain 19 residue 46 TYR Chi-restraints excluded: chain 19 residue 75 TYR Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 20 residue 13 ARG Chi-restraints excluded: chain 20 residue 15 SER Chi-restraints excluded: chain 20 residue 20 VAL Chi-restraints excluded: chain 20 residue 49 ILE Chi-restraints excluded: chain 20 residue 80 ARG Chi-restraints excluded: chain 20 residue 95 ASP Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 71 VAL Chi-restraints excluded: chain 21 residue 110 ARG Chi-restraints excluded: chain 22 residue 25 GLU Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 40 LEU Chi-restraints excluded: chain 23 residue 58 VAL Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 45 ASP Chi-restraints excluded: chain 24 residue 61 LEU Chi-restraints excluded: chain 25 residue 76 ILE Chi-restraints excluded: chain 26 residue 10 ARG Chi-restraints excluded: chain 26 residue 16 ASN Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 67 LEU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 35 ASP Chi-restraints excluded: chain 29 residue 48 GLN Chi-restraints excluded: chain 29 residue 66 ILE Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 21 LEU Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 31 GLU Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 32 residue 8 SER Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 84 ARG Chi-restraints excluded: chain N residue 100 TRP Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 71 SER Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain T residue 74 HIS Chi-restraints excluded: chain U residue 11 PHE Chi-restraints excluded: chain U residue 20 ARG Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 69 THR Chi-restraints excluded: chain 03 residue 178 VAL Chi-restraints excluded: chain 03 residue 180 PHE Chi-restraints excluded: chain 03 residue 192 LEU Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain 03 residue 225 ASP Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 65 SER Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 108 THR Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 159 GLN Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 320 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 693 optimal weight: 30.0000 chunk 930 optimal weight: 30.0000 chunk 267 optimal weight: 6.9990 chunk 805 optimal weight: 30.0000 chunk 128 optimal weight: 30.0000 chunk 242 optimal weight: 9.9990 chunk 874 optimal weight: 20.0000 chunk 366 optimal weight: 6.9990 chunk 898 optimal weight: 30.0000 chunk 110 optimal weight: 30.0000 chunk 161 optimal weight: 0.0970 overall best weight: 8.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 06 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.043360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.037160 restraints weight = 1622668.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.038124 restraints weight = 713629.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.038669 restraints weight = 406745.897| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.340 166780 Z= 0.273 Angle : 0.744 59.195 249021 Z= 0.391 Chirality : 0.040 0.699 31775 Planarity : 0.005 0.128 13713 Dihedral : 24.391 178.576 82259 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 31.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.87 % Favored : 86.85 % Rotamer: Outliers : 5.39 % Allowed : 26.91 % Favored : 67.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.10), residues: 6366 helix: -0.86 (0.11), residues: 1915 sheet: -2.16 (0.16), residues: 968 loop : -2.59 (0.10), residues: 3483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 169 HIS 0.019 0.002 HIS O 45 PHE 0.042 0.002 PHE15 117 TYR 0.024 0.002 TYR B 212 ARG 0.048 0.001 ARG G 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38465.36 seconds wall clock time: 677 minutes 47.95 seconds (40667.95 seconds total)