Starting phenix.real_space_refine (version: dev) on Tue May 24 11:27:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/05_2022/5uyp_8619_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/05_2022/5uyp_8619.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/05_2022/5uyp_8619_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/05_2022/5uyp_8619_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/05_2022/5uyp_8619_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/05_2022/5uyp_8619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/05_2022/5uyp_8619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/05_2022/5uyp_8619_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/05_2022/5uyp_8619_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.332 sd= 1.036 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 Convert atoms to be neutral 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 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 TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "12 ARG 96": "NH1" <-> "NH2" Residue "12 ARG 120": "NH1" <-> "NH2" Residue "13 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 93": "NH1" <-> "NH2" Residue "23 PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "31 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "03 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" 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-4597/modules/chem_data/mon_lib" Total number of atoms: 153780 Number of models: 1 Model: "" Number of chains: 63 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': 89, 'rna3p_pur': 785, 'rna2p_pyr': 47, 'rna3p_pyr': 618} Link IDs: {'rna3p': 1402, 'rna2p': 136} 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': 207, 'rna3p_pur': 1467, 'rna2p_pyr': 91, 'rna3p_pyr': 1138} Link IDs: {'rna3p': 2604, 'rna2p': 298} Chain: "02" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 53, 'rna2p_pur': 3, 'rna3p_pur': 62, 'rna2p_pyr': 2, '5*END': 1} Link IDs: {'rna3p': 114, 'rna2p': 5} Chain: "X" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'rna3p_pyr': 33, 'rna2p_pur': 5, 'rna3p_pur': 34, 'rna2p_pyr': 5, '5*END': 1} Link IDs: {'rna3p': 66, 'rna2p': 10} Chain: "V" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 417 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 15, 'rna3p_pyr': 2} Link IDs: {'rna3p': 17, 'rna2p': 1} Chain: "W" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'rna3p_pyr': 34, 'rna2p_pur': 6, 'rna3p_pur': 33, 'rna2p_pyr': 4, '5*END': 1} Link IDs: {'rna3p': 67, 'rna2p': 9} Chain: "Y" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1618 Classifications: {'RNA': 76} Modifications used: {'rna2p_pyr': 7, 'p5*END': 1, 'rna2p': 1, 'rna3p_pyr': 31, 'rna2p_pur': 8, 'rna3p_pur': 29} Link IDs: {'rna3p': 60, 'rna2p': 15} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "Z" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3029 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 371} 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 Chain: "W" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GCP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 62.01, per 1000 atoms: 0.40 Number of scatterers: 153780 At special positions: 0 Unit cell: (278.8, 266.5, 238.62, 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 173 16.00 P 4808 15.00 O 42503 8.00 N 28581 7.00 C 77715 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 52.94 Conformation dependent library (CDL) restraints added in 6.8 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: 11886 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 197 helices and 78 sheets defined 38.2% alpha, 18.3% beta 1427 base pairs and 2955 stacking pairs defined. Time for finding SS restraints: 64.17 Creating SS restraints... Processing helix chain '04' and resid 9 through 16 removed outlier: 7.813A pdb=" N HIS04 14 " --> pdb=" O PRO04 10 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL04 15 " --> pdb=" O GLY04 11 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL04 16 " --> pdb=" O ARG04 12 " (cutoff:3.500A) Processing helix chain '04' and resid 29 through 34 removed outlier: 4.194A pdb=" N LEU04 33 " --> pdb=" O PHE04 29 " (cutoff:3.500A) removed outlier: 5.428A 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 Proline residue: 04 135 - end of helix Processing helix chain '04' and resid 206 through 214 removed outlier: 4.203A pdb=" N ALA04 210 " --> pdb=" O LYS04 206 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG04 213 " --> pdb=" O ALA04 209 " (cutoff:3.500A) Processing helix chain '04' and resid 220 through 225 removed outlier: 4.322A pdb=" N MET04 224 " --> pdb=" O ARG04 220 " (cutoff:3.500A) removed outlier: 5.410A 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: 6.427A pdb=" N ASP04 263 " --> pdb=" O ASN04 259 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS04 264 " --> pdb=" O LYS04 260 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE04 265 " --> pdb=" O ARG04 261 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VAL04 267 " --> pdb=" O ASP04 263 " (cutoff:3.500A) Processing helix chain '04' and resid 196 through 201 removed outlier: 4.286A pdb=" N MET04 200 " --> pdb=" O ALA04 197 " (cutoff:3.500A) Processing helix chain '05' and resid 61 through 72 removed outlier: 3.548A pdb=" N HIS05 67 " --> pdb=" O PRO05 63 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA05 71 " --> pdb=" O HIS05 67 " (cutoff:3.500A) Processing helix chain '05' and resid 120 through 125 Processing helix chain '05' and resid 39 through 44 Processing helix chain '06' and resid 24 through 40 removed outlier: 3.789A pdb=" N ARG06 40 " --> pdb=" O ALA06 36 " (cutoff:3.500A) Processing helix chain '06' and resid 48 through 53 removed outlier: 5.926A pdb=" N THR06 53 " --> pdb=" O ARG06 49 " (cutoff:3.500A) Processing helix chain '06' and resid 97 through 116 removed outlier: 3.521A pdb=" N LEU06 105 " --> pdb=" O TYR06 101 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG06 114 " --> pdb=" O SER06 110 " (cutoff:3.500A) Processing helix chain '06' and resid 130 through 142 removed outlier: 3.590A pdb=" N LYS06 137 " --> pdb=" O LEU06 133 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS06 139 " --> pdb=" O ALA06 135 " (cutoff:3.500A) Processing helix chain '06' and resid 154 through 163 removed outlier: 3.829A pdb=" N ALA06 160 " --> pdb=" O ASN06 156 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN06 163 " --> pdb=" O LEU06 159 " (cutoff:3.500A) Processing helix chain '06' and resid 176 through 182 removed outlier: 3.788A pdb=" N LEU06 180 " --> pdb=" O ASP06 176 " (cutoff:3.500A) Processing helix chain '06' and resid 189 through 201 removed outlier: 3.598A pdb=" N GLN06 195 " --> pdb=" O ASP06 191 " (cutoff:3.500A) Processing helix chain '06' and resid 15 through 21 removed outlier: 3.889A pdb=" N GLY06 20 " --> pdb=" O SER06 15 " (cutoff:3.500A) Processing helix chain '07' and resid 1 through 20 removed outlier: 3.563A pdb=" N VAL07 11 " --> pdb=" O TYR07 7 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL07 12 " --> pdb=" O LYS07 8 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS07 13 " --> pdb=" O ASP07 9 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR07 17 " --> pdb=" O LYS07 13 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU07 18 " --> pdb=" O LYS07 14 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN07 20 " --> pdb=" O MET07 16 " (cutoff:3.500A) Processing helix chain '07' and resid 41 through 46 removed outlier: 3.534A pdb=" N ASP07 45 " --> pdb=" O GLU07 41 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS07 46 " --> pdb=" O ALA07 42 " (cutoff:3.500A) No H-bonds generated for 'chain '07' and resid 41 through 46' Processing helix chain '07' and resid 47 through 61 Processing helix chain '07' and resid 92 through 109 removed outlier: 4.420A pdb=" N TRP07 96 " --> pdb=" O GLY07 92 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE07 99 " --> pdb=" O MET07 95 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE07 105 " --> pdb=" O ARG07 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL07 107 " --> pdb=" O ILE07 103 " (cutoff:3.500A) Proline residue: 07 108 - end of helix Processing helix chain '07' and resid 133 through 138 removed outlier: 5.301A pdb=" N PHE07 137 " --> pdb=" O GLU07 133 " (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 '07' and resid 161 through 173 removed outlier: 3.804A pdb=" N ALA07 167 " --> pdb=" O GLU07 163 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE07 172 " --> pdb=" O LEU07 168 " (cutoff:3.500A) Processing helix chain '08' and resid 1 through 6 removed outlier: 4.443A pdb=" N ALA08 6 " --> pdb=" O ARG08 2 " (cutoff:3.500A) Processing helix chain '08' and resid 59 through 80 removed outlier: 3.962A pdb=" N ALA08 69 " --> pdb=" O GLY08 65 " (cutoff:3.500A) Processing helix chain '08' and resid 136 through 152 removed outlier: 3.608A pdb=" N ALA08 149 " --> pdb=" O ALA08 145 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG08 151 " --> pdb=" O LEU08 147 " (cutoff:3.500A) Processing helix chain '09' and resid 22 through 27 Processing helix chain '09' and resid 29 through 34 removed outlier: 3.662A pdb=" N GLN09 33 " --> pdb=" O PHE09 29 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY09 34 " --> pdb=" O LEU09 30 " (cutoff:3.500A) No H-bonds generated for 'chain '09' and resid 29 through 34' Processing helix chain '09' and resid 40 through 50 removed outlier: 3.688A pdb=" N GLU09 48 " --> pdb=" O ILE09 44 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA09 49 " --> pdb=" O GLU09 45 " (cutoff:3.500A) Processing helix chain '09' and resid 53 through 74 removed outlier: 5.446A pdb=" N LYS09 57 " --> pdb=" O GLU09 53 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU09 62 " --> pdb=" O LEU09 58 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA09 67 " --> pdb=" O ALA09 63 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN09 73 " --> pdb=" O ALA09 69 " (cutoff:3.500A) Processing helix chain '09' and resid 95 through 107 removed outlier: 3.500A pdb=" N ILE09 99 " --> pdb=" O GLY09 95 " (cutoff:3.500A) Processing helix chain '09' and resid 111 through 116 removed outlier: 3.993A pdb=" N VAL09 115 " --> pdb=" O ALA09 111 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG09 116 " --> pdb=" O LYS09 112 " (cutoff:3.500A) No H-bonds generated for 'chain '09' and resid 111 through 116' Processing helix chain '10' and resid 3 through 21 removed outlier: 3.909A pdb=" N LYS10 8 " --> pdb=" O ASN10 4 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU10 17 " --> pdb=" O ALA10 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS10 20 " --> pdb=" O SER10 16 " (cutoff:3.500A) Processing helix chain '10' and resid 33 through 48 removed outlier: 5.651A pdb=" N ARG10 42 " --> pdb=" O MET10 38 " (cutoff:3.500A) Processing helix chain '10' and resid 62 through 71 removed outlier: 3.929A pdb=" N GLY10 66 " --> pdb=" O ARG10 62 " (cutoff:3.500A) Proline residue: 10 68 - end of helix removed outlier: 4.244A pdb=" N CYS10 71 " --> pdb=" O THR10 67 " (cutoff:3.500A) Processing helix chain '10' and resid 94 through 106 removed outlier: 3.604A pdb=" N PHE10 99 " --> pdb=" O LEU10 95 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA10 104 " --> pdb=" O ALA10 100 " (cutoff:3.500A) Processing helix chain '10' and resid 72 through 78 removed outlier: 4.369A pdb=" N PHE10 76 " --> pdb=" O LYS10 73 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY10 78 " --> pdb=" O ALA10 75 " (cutoff:3.500A) Processing helix chain '11' and resid 21 through 31 Proline residue: 11 25 - end of helix removed outlier: 4.517A pdb=" N GLN11 30 " --> pdb=" O ALA11 26 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY11 31 " --> pdb=" O LEU11 27 " (cutoff:3.500A) Processing helix chain '11' and resid 33 through 48 removed outlier: 3.649A pdb=" N PHE11 37 " --> pdb=" O ASN11 33 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA11 40 " --> pdb=" O GLU11 36 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER11 47 " --> pdb=" O ALA11 43 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE11 48 " --> pdb=" O LYS11 44 " (cutoff:3.500A) Processing helix chain '11' and resid 74 through 84 removed outlier: 3.934A pdb=" N LYS11 80 " --> pdb=" O ALA11 76 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA11 83 " --> pdb=" O LEU11 79 " (cutoff:3.500A) Processing helix chain '11' and resid 101 through 114 removed outlier: 4.128A pdb=" N GLU11 107 " --> pdb=" O ALA11 103 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA11 114 " --> pdb=" O GLN11 110 " (cutoff:3.500A) Processing helix chain '11' and resid 120 through 136 removed outlier: 3.968A pdb=" N MET11 124 " --> pdb=" O ASP11 120 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG11 126 " --> pdb=" O GLU11 122 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER11 127 " --> pdb=" O ALA11 123 " (cutoff:3.500A) Processing helix chain '12' and resid 24 through 38 removed outlier: 3.721A pdb=" N GLU12 31 " --> pdb=" O ARG12 27 " (cutoff:3.500A) Processing helix chain '12' and resid 67 through 72 Processing helix chain '12' and resid 88 through 96 removed outlier: 3.733A pdb=" N ALA12 94 " --> pdb=" O GLU12 90 " (cutoff:3.500A) Processing helix chain '12' and resid 97 through 110 removed outlier: 4.507A pdb=" N ILE12 101 " --> pdb=" O PRO12 97 " (cutoff:3.500A) removed outlier: 3.859A 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: 3.829A pdb=" N PHE12 119 " --> pdb=" O GLY12 115 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG12 120 " --> pdb=" O ARG12 116 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS12 121 " --> pdb=" O ALA12 117 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU12 122 " --> pdb=" O MET12 118 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS12 123 " --> pdb=" O PHE12 119 " (cutoff:3.500A) Processing helix chain '13' and resid 112 through 120 removed outlier: 3.718A pdb=" N ILE13 116 " --> pdb=" O PHE13 112 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU13 118 " --> pdb=" O LYS13 114 " (cutoff:3.500A) Proline residue: 13 120 - end of helix Processing helix chain '13' and resid 104 through 109 removed outlier: 4.713A pdb=" N SER13 109 " --> pdb=" O GLU13 106 " (cutoff:3.500A) Processing helix chain '14' and resid 37 through 42 removed outlier: 5.888A pdb=" N SER14 42 " --> pdb=" O GLN14 38 " (cutoff:3.500A) 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: 3.663A pdb=" N ALA14 72 " --> pdb=" O SER14 68 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE14 73 " --> pdb=" O ARG14 69 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR14 74 " --> pdb=" O LYS14 70 " (cutoff:3.500A) removed outlier: 5.707A 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 86 removed outlier: 3.750A pdb=" N LEU14 82 " --> pdb=" O ARG14 78 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA14 83 " --> pdb=" O LEU14 79 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS14 84 " --> pdb=" O SER14 80 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL14 85 " --> pdb=" O ASP14 81 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU14 86 " --> pdb=" O LEU14 82 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 78 through 86' Processing helix chain '14' and resid 93 through 99 removed outlier: 5.700A pdb=" N ALA14 97 " --> pdb=" O ASN14 93 " (cutoff:3.500A) Processing helix chain '14' and resid 128 through 139 removed outlier: 3.681A pdb=" N ALA14 133 " --> pdb=" O LYS14 129 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA14 138 " --> pdb=" O ALA14 134 " (cutoff:3.500A) Processing helix chain '15' and resid 42 through 58 removed outlier: 4.231A pdb=" N ALA15 52 " --> pdb=" O ALA15 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL15 57 " --> pdb=" O MET15 53 " (cutoff:3.500A) Processing helix chain '15' and resid 109 through 125 removed outlier: 3.606A pdb=" N GLU15 115 " --> pdb=" O GLU15 111 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE15 117 " --> pdb=" O ALA15 113 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS15 118 " --> pdb=" O ARG15 114 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU15 119 " --> pdb=" O GLU15 115 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA15 120 " --> pdb=" O ALA15 116 " (cutoff:3.500A) removed outlier: 3.872A 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: 3.581A pdb=" N MET16 24 " --> pdb=" O MET16 20 " (cutoff:3.500A) Processing helix chain '16' and resid 38 through 57 removed outlier: 3.555A pdb=" N ARG16 45 " --> pdb=" O ALA16 41 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG16 46 " --> pdb=" O LYS16 42 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL16 47 " --> pdb=" O GLU16 43 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU16 49 " --> pdb=" O ARG16 45 " (cutoff:3.500A) Proline residue: 16 50 - end of helix removed outlier: 3.924A pdb=" N LYS16 56 " --> pdb=" O ILE16 52 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR16 57 " --> pdb=" O THR16 53 " (cutoff:3.500A) Processing helix chain '16' and resid 59 through 71 removed outlier: 3.884A pdb=" N ARG16 63 " --> pdb=" O SER16 59 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N THR16 70 " --> pdb=" O ALA16 66 " (cutoff:3.500A) Processing helix chain '16' and resid 72 through 81 removed outlier: 3.595A pdb=" N VAL16 76 " --> pdb=" O ASP16 72 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE16 80 " --> pdb=" O VAL16 76 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN16 81 " --> pdb=" O ALA16 77 " (cutoff:3.500A) Processing helix chain '16' and resid 82 through 89 removed outlier: 4.130A pdb=" N ARG16 86 " --> pdb=" O GLU16 82 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA16 88 " --> pdb=" O GLY16 84 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER16 89 " --> pdb=" O PRO16 85 " (cutoff:3.500A) Processing helix chain '17' and resid 3 through 22 removed outlier: 3.717A pdb=" N ARG17 7 " --> pdb=" O LYS17 3 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR17 12 " --> pdb=" O ILE17 8 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG17 13 " --> pdb=" O ARG17 9 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA17 14 " --> pdb=" O ARG17 10 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG17 15 " --> pdb=" O ALA17 11 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS17 17 " --> pdb=" O ARG17 13 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY17 22 " --> pdb=" O LEU17 18 " (cutoff:3.500A) Processing helix chain '17' and resid 55 through 63 removed outlier: 3.611A pdb=" N GLU17 60 " --> pdb=" O LYS17 56 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLN17 61 " --> pdb=" O ALA17 57 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU17 62 " --> pdb=" O ILE17 58 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LYS17 63 " --> pdb=" O ALA17 59 " (cutoff:3.500A) Processing helix chain '17' and resid 67 through 86 removed outlier: 3.524A pdb=" N VAL17 74 " --> pdb=" O ALA17 70 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY17 75 " --> pdb=" O ALA17 71 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS17 76 " --> pdb=" O ALA17 72 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU17 83 " --> pdb=" O ALA17 79 " (cutoff:3.500A) Processing helix chain '17' and resid 101 through 114 removed outlier: 3.575A pdb=" N GLU17 112 " --> pdb=" O ASP17 108 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA17 113 " --> pdb=" O ALA17 109 " (cutoff:3.500A) Processing helix chain '18' and resid 1 through 13 removed outlier: 3.732A pdb=" N GLU18 10 " --> pdb=" O GLN18 6 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN18 11 " --> pdb=" O LEU18 7 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET18 12 " --> pdb=" O GLU18 8 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS18 13 " --> pdb=" O GLN18 9 " (cutoff:3.500A) Processing helix chain '18' and resid 96 through 103 removed outlier: 4.739A pdb=" N ARG18 100 " --> pdb=" O LEU18 96 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU18 101 " --> pdb=" O TYR18 97 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG18 102 " --> pdb=" O TYR18 98 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N THR18 103 " --> pdb=" O LEU18 99 " (cutoff:3.500A) No H-bonds generated for 'chain '18' and resid 96 through 103' Processing helix chain '19' and resid 5 through 21 removed outlier: 3.841A pdb=" N ALA19 9 " --> pdb=" O ARG19 5 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN19 19 " --> pdb=" O LYS19 15 " (cutoff:3.500A) Processing helix chain '19' and resid 25 through 30 removed outlier: 3.708A pdb=" N ARG19 29 " --> pdb=" O GLY19 25 " (cutoff:3.500A) Processing helix chain '19' and resid 39 through 60 removed outlier: 3.574A pdb=" N ARG19 50 " --> pdb=" O TYR19 46 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS19 53 " --> pdb=" O ARG19 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG19 54 " --> pdb=" O ARG19 50 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.893A pdb=" N ASP19 96 " --> pdb=" O LYS19 92 " (cutoff:3.500A) Processing helix chain '19' and resid 102 through 117 removed outlier: 3.680A pdb=" N ALA19 115 " --> pdb=" O LYS19 111 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU19 116 " --> pdb=" O ALA19 112 " (cutoff:3.500A) Processing helix chain '21' and resid 13 through 22 removed outlier: 3.548A pdb=" N LEU21 19 " --> pdb=" O GLN21 15 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL21 20 " --> pdb=" O LYS21 16 " (cutoff:3.500A) Processing helix chain '21' and resid 28 through 40 removed outlier: 4.012A pdb=" N ASP21 34 " --> pdb=" O SER21 30 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASN21 40 " --> pdb=" O LEU21 36 " (cutoff:3.500A) Processing helix chain '21' and resid 41 through 60 removed outlier: 3.704A pdb=" N LYS21 48 " --> pdb=" O ALA21 44 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS21 49 " --> pdb=" O VAL21 45 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL21 50 " --> pdb=" O LEU21 46 " (cutoff:3.500A) Processing helix chain '22' and resid 2 through 11 removed outlier: 4.626A pdb=" N LYS22 9 " --> pdb=" O GLU22 5 " (cutoff:3.500A) removed outlier: 4.527A 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 51 Processing helix chain '23' and resid 35 through 40 removed outlier: 4.222A pdb=" N ASN23 39 " --> pdb=" O VAL23 35 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU23 40 " --> pdb=" O GLU23 36 " (cutoff:3.500A) No H-bonds generated for 'chain '23' and resid 35 through 40' Processing helix chain '23' and resid 65 through 70 removed outlier: 4.267A pdb=" N VAL23 69 " --> pdb=" O GLN23 65 " (cutoff:3.500A) removed outlier: 5.420A 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: 3.559A pdb=" N ARG24 18 " --> pdb=" O LYS24 14 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG24 19 " --> pdb=" O GLY24 15 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN24 24 " --> pdb=" O LEU24 20 " (cutoff:3.500A) Processing helix chain '24' and resid 44 through 54 removed outlier: 3.560A pdb=" N ALA24 52 " --> pdb=" O MET24 48 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS24 53 " --> pdb=" O ASN24 49 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ALA24 54 " --> pdb=" O MET24 50 " (cutoff:3.500A) Processing helix chain '26' and resid 51 through 61 removed outlier: 3.522A pdb=" N MET26 55 " --> pdb=" O SER26 51 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG26 56 " --> pdb=" O ALA26 52 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL26 57 " --> pdb=" O LYS26 53 " (cutoff:3.500A) Processing helix chain '26' and resid 62 through 74 removed outlier: 3.944A pdb=" N LEU26 70 " --> pdb=" O VAL26 66 " (cutoff:3.500A) Processing helix chain '27' and resid 1 through 7 removed outlier: 3.625A pdb=" N GLU27 5 " --> pdb=" O MET27 1 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU27 6 " --> pdb=" O LYS27 2 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG27 7 " --> pdb=" O ALA27 3 " (cutoff:3.500A) No H-bonds generated for 'chain '27' and resid 1 through 7' Processing helix chain '27' and resid 9 through 35 removed outlier: 3.704A pdb=" N THR27 16 " --> pdb=" O GLU27 12 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG27 23 " --> pdb=" O LEU27 19 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN27 25 " --> pdb=" O LEU27 21 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE27 26 " --> pdb=" O LEU27 22 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU27 28 " --> pdb=" O GLU27 24 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA27 32 " --> pdb=" O LEU27 28 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER27 34 " --> pdb=" O MET27 30 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY27 35 " --> pdb=" O GLN27 31 " (cutoff:3.500A) Processing helix chain '27' and resid 40 through 62 removed outlier: 3.924A pdb=" N LYS27 44 " --> pdb=" O SER27 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN27 58 " --> pdb=" O LYS27 54 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY27 62 " --> pdb=" O ASN27 58 " (cutoff:3.500A) Processing helix chain '28' and resid 16 through 27 removed outlier: 3.581A pdb=" N THR28 22 " --> pdb=" O LYS28 18 " (cutoff:3.500A) Processing helix chain '28' and resid 40 through 51 removed outlier: 3.817A pdb=" N MET28 46 " --> pdb=" O ALA28 42 " (cutoff:3.500A) Processing helix chain '29' and resid 43 through 51 removed outlier: 4.620A pdb=" N GLN29 48 " --> pdb=" O PHE29 44 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP29 50 " --> pdb=" O GLY29 46 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL29 51 " --> pdb=" O LYS29 47 " (cutoff:3.500A) Processing helix chain '29' and resid 55 through 65 removed outlier: 5.438A pdb=" N ARG29 59 " --> pdb=" O GLY29 55 " (cutoff:3.500A) Processing helix chain '30' and resid 8 through 20 removed outlier: 4.559A pdb=" N HIS30 18 " --> pdb=" O MET30 14 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP30 19 " --> pdb=" O ARG30 15 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA30 20 " --> pdb=" O ARG30 16 " (cutoff:3.500A) Processing helix chain '32' and resid 8 through 16 Processing helix chain '32' and resid 17 through 24 removed outlier: 4.680A pdb=" N THR32 24 " --> pdb=" O ALA32 20 " (cutoff:3.500A) Processing helix chain '32' and resid 25 through 38 removed outlier: 3.993A pdb=" N ARG32 33 " --> pdb=" O GLN32 29 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG32 35 " --> pdb=" O LEU32 31 " (cutoff:3.500A) Processing helix chain '33' and resid 6 through 13 removed outlier: 3.620A pdb=" N ALA33 10 " --> pdb=" O VAL33 6 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS33 11 " --> pdb=" O ARG33 7 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG33 12 " --> pdb=" O GLY33 8 " (cutoff:3.500A) Processing helix chain '33' and resid 31 through 36 removed outlier: 5.036A pdb=" N LYS33 35 " --> pdb=" O ILE33 31 " (cutoff:3.500A) removed outlier: 5.242A 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: 4.043A pdb=" N GLY33 55 " --> pdb=" O LYS33 51 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU33 56 " --> pdb=" O GLY33 52 " (cutoff:3.500A) Proline residue: 33 62 - end of helix Processing helix chain '34' and resid 30 through 35 removed outlier: 4.413A pdb=" N GLN34 35 " --> pdb=" O LYS34 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 63 removed outlier: 3.765A pdb=" N VAL B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 3.669A pdb=" N ASN B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 86 removed outlier: 5.662A pdb=" N SER B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 122 removed outlier: 4.281A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.677A pdb=" N MET B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 removed outlier: 4.466A pdb=" N ASP B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLY B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 154' Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.734A pdb=" N ILE B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 225 removed outlier: 4.675A pdb=" N THR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.557A pdb=" N ILE C 9 " --> pdb=" O HIS C 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.518A pdb=" N GLN C 40 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.546A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 removed outlier: 4.113A pdb=" N GLU C 84 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.871A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 107 through 112' Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.167A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 removed outlier: 3.553A pdb=" N ALA C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 4.462A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 Processing helix chain 'D' and resid 67 through 82 removed outlier: 5.578A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 4.278A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 removed outlier: 3.596A pdb=" N GLY D 105 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 120 removed outlier: 3.508A pdb=" N ARG D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 removed outlier: 6.561A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.623A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 removed outlier: 4.075A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 6.239A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 114 " --> pdb=" O MET E 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.549A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP E 141 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 156 Processing helix chain 'E' and resid 159 through 165 Processing helix chain 'F' and resid 14 through 33 removed outlier: 3.745A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.816A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.618A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN F 81 " --> pdb=" O THR F 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 removed outlier: 3.632A pdb=" N PHE G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 54 removed outlier: 3.827A pdb=" N SER G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 69 removed outlier: 3.763A pdb=" N ALA G 60 " --> pdb=" O SER G 56 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 4.077A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 Processing helix chain 'G' and resid 131 through 147 removed outlier: 3.554A pdb=" N ARG G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU G 145 " --> pdb=" O HIS G 141 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 20 removed outlier: 3.686A pdb=" N ALA H 18 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 43 removed outlier: 3.627A pdb=" N GLY H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.599A pdb=" N GLN H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 38 removed outlier: 4.067A pdb=" N PHE I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 52 removed outlier: 4.534A 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: 3.585A pdb=" N GLN I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA I 75 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA I 77 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 101 removed outlier: 3.918A pdb=" N ARG I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 31 removed outlier: 3.563A pdb=" N ALA J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU J 24 " --> pdb=" O GLN J 20 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG J 31 " --> pdb=" O GLU J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 88 removed outlier: 3.946A pdb=" N VAL J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 removed outlier: 3.569A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 45 through 50' Processing helix chain 'K' and resid 53 through 58 removed outlier: 3.693A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 53 through 58' Processing helix chain 'K' and resid 59 through 75 removed outlier: 3.549A pdb=" N ASP K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLU K 75 " --> pdb=" O ASP K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 removed outlier: 5.438A pdb=" N THR K 95 " --> pdb=" O GLY K 91 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA K 101 " --> pdb=" O ARG K 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 removed outlier: 3.653A pdb=" N ARG L 8 " --> pdb=" O ASN L 4 " (cutoff:3.500A) Proline residue: L 10 - end of helix Processing helix chain 'L' and resid 21 through 26 removed outlier: 7.038A pdb=" N ALA L 25 " --> pdb=" O PRO L 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 21 through 26' Processing helix chain 'L' and resid 112 through 117 removed outlier: 4.828A pdb=" N TYR L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 4.361A 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: 3.702A pdb=" N SER M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.505A pdb=" N ALA M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 48 removed outlier: 5.407A pdb=" N SER M 48 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 63 removed outlier: 5.031A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA M 60 " --> pdb=" O ARG M 56 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL M 63 " --> pdb=" O VAL M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 removed outlier: 4.341A pdb=" N ARG M 70 " --> pdb=" O GLY M 66 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 93 Processing helix chain 'M' and resid 105 through 110 Processing helix chain 'N' and resid 2 through 23 removed outlier: 3.510A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA N 21 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS N 22 " --> pdb=" O LYS N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 29 Processing helix chain 'N' and resid 37 through 50 removed outlier: 4.902A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 removed outlier: 5.152A pdb=" N ARG N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 3.882A pdb=" N GLU N 85 " --> pdb=" O ILE N 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 23 through 46 removed outlier: 3.515A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU O 44 " --> pdb=" O GLY O 40 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N HIS O 45 " --> pdb=" O HIS O 41 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS O 46 " --> pdb=" O PHE O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 73 removed outlier: 4.116A pdb=" N ARG O 53 " --> pdb=" O HIS O 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR O 68 " --> pdb=" O LYS O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.757A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY O 85 " --> pdb=" O ILE O 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.708A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 79 removed outlier: 3.544A pdb=" N LYS P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN P 79 " --> pdb=" O ILE P 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 6.843A pdb=" N GLU R 15 " --> pdb=" O ARG R 11 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY R 16 " --> pdb=" O PHE R 12 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL R 17 " --> pdb=" O THR R 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 11 through 17' Processing helix chain 'R' and resid 24 through 33 removed outlier: 4.063A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N THR R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.821A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 65 removed outlier: 4.024A pdb=" N LEU R 64 " --> pdb=" O ARG R 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 25 removed outlier: 3.988A pdb=" N GLU S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER S 24 " --> pdb=" O LYS S 20 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 75 removed outlier: 4.490A pdb=" N PHE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) Proline residue: S 75 - end of helix Processing helix chain 'T' and resid 5 through 41 removed outlier: 4.949A pdb=" N ARG T 9 " --> pdb=" O SER T 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU T 14 " --> pdb=" O ALA T 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS T 18 " --> pdb=" O GLU T 14 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 64 removed outlier: 3.548A pdb=" N ALA T 46 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Proline residue: T 55 - end of helix removed outlier: 3.891A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA T 62 " --> pdb=" O ASP T 58 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS T 63 " --> pdb=" O ARG T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 86 removed outlier: 5.806A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU T 78 " --> pdb=" O HIS T 74 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 34 removed outlier: 4.086A pdb=" N ARG U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LYS U 24 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N ALA U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY U 26 " --> pdb=" O CYS U 22 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL U 27 " --> pdb=" O GLU U 23 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU U 28 " --> pdb=" O LYS U 24 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 61 Proline residue: U 40 - end of helix removed outlier: 3.619A pdb=" N ARG U 44 " --> pdb=" O PRO U 40 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS U 55 " --> pdb=" O ALA U 51 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU U 59 " --> pdb=" O HIS U 55 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG U 61 " --> pdb=" O LYS U 57 " (cutoff:3.500A) Processing helix chain '03' and resid 5 through 14 removed outlier: 4.277A pdb=" N VAL03 10 " --> pdb=" O LYS03 6 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG03 12 " --> pdb=" O MET03 8 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU03 13 " --> pdb=" O ARG03 9 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS03 14 " --> pdb=" O VAL03 10 " (cutoff:3.500A) Processing helix chain '03' and resid 22 through 34 removed outlier: 3.617A pdb=" N ALA03 26 " --> pdb=" O ASP03 22 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE03 27 " --> pdb=" O ILE03 23 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ALA03 28 " --> pdb=" O ASN03 24 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU03 30 " --> pdb=" O ALA03 26 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS03 31 " --> pdb=" O ILE03 27 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU03 32 " --> pdb=" O ALA03 28 " (cutoff:3.500A) Processing helix chain '03' and resid 181 through 200 removed outlier: 3.940A pdb=" N ASN03 188 " --> pdb=" O LYS03 184 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA03 199 " --> pdb=" O ALA03 195 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS03 200 " --> pdb=" O LEU03 196 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 37 removed outlier: 3.661A pdb=" N THR Z 32 " --> pdb=" O THR Z 28 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU Z 35 " --> pdb=" O ILE Z 31 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS Z 37 " --> pdb=" O THR Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 51 removed outlier: 4.106A 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 85 through 96 removed outlier: 4.232A pdb=" N LYS Z 89 " --> pdb=" O ALA Z 85 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN Z 90 " --> pdb=" O ASP Z 86 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR Z 93 " --> pdb=" O LYS Z 89 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY Z 94 " --> pdb=" O ASN Z 90 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 126 removed outlier: 3.625A pdb=" N HIS Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG Z 123 " --> pdb=" O ILE Z 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY Z 126 " --> pdb=" O GLY Z 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 136 through 141 removed outlier: 4.322A pdb=" N VAL Z 140 " --> pdb=" O LYS Z 136 " (cutoff:3.500A) removed outlier: 4.645A 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: 3.672A pdb=" N LEU Z 146 " --> pdb=" O ASP Z 142 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU Z 148 " --> pdb=" O GLU Z 144 " (cutoff:3.500A) Processing helix chain 'Z' and resid 173 through 180 removed outlier: 3.685A pdb=" N ALA Z 177 " --> pdb=" O SER Z 173 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY Z 180 " --> pdb=" O LYS Z 176 " (cutoff:3.500A) Processing helix chain 'Z' and resid 181 through 199 removed outlier: 3.522A pdb=" N LEU Z 191 " --> pdb=" O LYS Z 187 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP Z 196 " --> pdb=" O ALA Z 192 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE Z 199 " --> pdb=" O LEU Z 195 " (cutoff:3.500A) Processing helix chain 'Z' and resid 282 through 287 removed outlier: 3.876A pdb=" N ILE Z 286 " --> pdb=" O LYS Z 282 " (cutoff:3.500A) removed outlier: 5.275A 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: 6.896A pdb=" N LEU04 92 " --> pdb=" O GLU04 78 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP04 113 " --> pdb=" O VAL04 77 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '04' and resid 161 through 164 removed outlier: 6.634A pdb=" N THR04 172 " --> pdb=" O VAL04 164 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU04 179 " --> pdb=" O LEU04 175 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '04' and resid 90 through 95 removed outlier: 4.020A pdb=" N GLU04 99 " --> pdb=" O TYR04 95 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '05' and resid 3 through 8 removed outlier: 4.442A pdb=" N SER05 199 " --> pdb=" O LYS05 8 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP05 200 " --> pdb=" O THR05 112 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR05 112 " --> pdb=" O ASP05 200 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL05 170 " --> pdb=" O GLY05 111 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '05' and resid 11 through 16 removed outlier: 4.241A pdb=" N VAL05 20 " --> pdb=" O THR05 16 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG05 179 " --> pdb=" O LEU05 188 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '05' and resid 79 through 84 removed outlier: 6.011A pdb=" N ARG05 46 " --> pdb=" O LEU05 84 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN05 49 " --> pdb=" O THR05 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL05 34 " --> pdb=" O GLN05 94 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN05 94 " --> pdb=" O VAL05 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '05' and resid 105 through 108 removed outlier: 6.515A pdb=" N LYS05 105 " --> pdb=" O VAL05 177 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '06' and resid 1 through 5 removed outlier: 4.399A 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: 5.424A pdb=" N ARG06 117 " --> pdb=" O ASP06 184 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '07' and resid 64 through 68 removed outlier: 3.590A pdb=" N CYS07 86 " --> pdb=" O MET07 37 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY07 38 " --> pdb=" O GLY07 150 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLY07 150 " --> pdb=" O GLY07 38 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '07' and resid 71 through 74 removed outlier: 5.039A pdb=" N SER07 72 " --> pdb=" O ARG07 79 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG07 79 " --> pdb=" O SER07 72 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA07 74 " --> pdb=" O LYS07 77 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '08' and resid 7 through 10 removed outlier: 3.564A pdb=" N VAL08 8 " --> pdb=" O LEU08 49 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASN08 47 " --> pdb=" O VAL08 10 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '08' and resid 15 through 18 removed outlier: 3.669A pdb=" N LYS08 26 " --> pdb=" O ASP08 15 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS08 17 " --> pdb=" O THR08 24 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '08' and resid 81 through 88 removed outlier: 3.777A pdb=" N GLY08 134 " --> pdb=" O PHE08 82 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR08 128 " --> pdb=" O LEU08 88 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS08 133 " --> pdb=" O THR08 121 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '08' and resid 94 through 98 removed outlier: 3.671A pdb=" N ARG08 94 " --> pdb=" O SER08 105 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL08 101 " --> pdb=" O LYS08 98 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASN08 100 " --> pdb=" O LEU08 116 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU08 116 " --> pdb=" O ASN08 100 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '09' and resid 2 through 6 removed outlier: 6.951A pdb=" N GLN09 2 " --> pdb=" O ALA09 39 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LYS09 35 " --> pdb=" O LEU09 6 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '09' and resid 76 through 83 removed outlier: 5.502A pdb=" N GLU09 76 " --> pdb=" O LYS09 141 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN09 145 " --> pdb=" O VAL09 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '10' and resid 22 through 28 No H-bonds generated for sheet with id= 18 Processing sheet with id= 19, first strand: chain '11' and resid 5 through 11 removed outlier: 3.783A pdb=" N LEU11 10 " --> pdb=" O VAL11 56 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL11 56 " --> pdb=" O LEU11 10 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR11 59 " --> pdb=" O THR11 67 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR11 67 " --> pdb=" O THR11 59 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '12' and resid 52 through 57 removed outlier: 5.436A pdb=" N ASP12 19 " --> pdb=" O LEU12 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '12' and resid 74 through 78 removed outlier: 3.732A pdb=" N ALA12 87 " --> pdb=" O TYR12 74 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS12 76 " --> pdb=" O LYS12 85 " (cutoff:3.500A) removed outlier: 7.118A 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: 6.615A pdb=" N ARG13 17 " --> pdb=" O VAL13 10 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL13 10 " --> pdb=" O ARG13 17 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR13 6 " --> pdb=" O CYS13 21 " (cutoff:3.500A) removed outlier: 6.164A 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: 4.039A pdb=" N TYR15 91 " --> pdb=" O ILE15 73 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '15' and resid 62 through 66 removed outlier: 5.722A pdb=" N LEU15 102 " --> pdb=" O ARG15 66 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR15 103 " --> pdb=" O LEU15 33 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER15 30 " --> pdb=" O LYS15 133 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS15 127 " --> pdb=" O VAL15 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '17' and resid 49 through 52 removed outlier: 3.700A pdb=" N VAL17 49 " --> pdb=" O VAL17 39 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG17 25 " --> pdb=" O ILE17 40 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL17 28 " --> pdb=" O ASP17 93 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '18' and resid 41 through 44 removed outlier: 6.229A pdb=" N THR18 24 " --> pdb=" O LYS18 86 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '18' and resid 57 through 63 Processing sheet with id= 28, first strand: chain '20' and resid 11 through 14 removed outlier: 3.640A pdb=" N TYR20 2 " --> pdb=" O ALA20 42 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET20 40 " --> pdb=" O VAL20 4 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '20' and resid 19 through 23 removed outlier: 6.595A pdb=" N ASP20 95 " --> pdb=" O VAL20 64 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS20 60 " --> pdb=" O THR20 99 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL20 33 " --> pdb=" O ALA20 61 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '20' and resid 57 through 60 removed outlier: 4.159A pdb=" N VAL20 58 " --> pdb=" O SER20 102 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER20 102 " --> pdb=" O VAL20 58 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '20' and resid 65 through 69 removed outlier: 3.918A pdb=" N GLY20 67 " --> pdb=" O PHE20 93 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN20 91 " --> pdb=" O GLY20 69 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '20' and resid 71 through 78 removed outlier: 4.266A pdb=" N TYR20 83 " --> pdb=" O ARG20 78 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '21' and resid 2 through 8 removed outlier: 4.137A pdb=" N THR21 3 " --> pdb=" O VAL21 107 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL21 107 " --> pdb=" O THR21 3 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL21 106 " --> pdb=" O THR21 72 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '21' and resid 73 through 79 removed outlier: 5.369A pdb=" N THR21 100 " --> pdb=" O GLY21 79 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '21' and resid 80 through 88 Processing sheet with id= 36, first strand: chain '22' and resid 12 through 15 removed outlier: 5.077A pdb=" N VAL22 31 " --> pdb=" O HIS22 15 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASN22 28 " --> pdb=" O LEU22 87 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS22 81 " --> pdb=" O VAL22 34 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS22 66 " --> pdb=" O ARG22 77 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP22 79 " --> pdb=" O LYS22 64 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS22 64 " --> pdb=" O ASP22 79 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS22 81 " --> pdb=" O VAL22 62 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL22 62 " --> pdb=" O LYS22 81 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA22 83 " --> pdb=" O THR22 60 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR22 60 " --> pdb=" O ALA22 83 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL22 85 " --> pdb=" O VAL22 58 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL22 58 " --> pdb=" O VAL22 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '23' and resid 8 through 12 removed outlier: 5.213A pdb=" N ASP23 8 " --> pdb=" O VAL23 24 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LYS23 20 " --> pdb=" O VAL23 12 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '23' and resid 41 through 44 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain '23' and resid 81 through 86 removed outlier: 5.180A pdb=" N ARG23 81 " --> pdb=" O LYS23 96 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '24' and resid 69 through 72 removed outlier: 3.652A pdb=" N VAL24 72 " --> pdb=" O LEU24 61 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASN24 5 " --> pdb=" O ASP24 43 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP24 43 " --> pdb=" O ASN24 5 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA24 39 " --> pdb=" O ARG24 9 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE24 89 " --> pdb=" O PRO24 27 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '25' and resid 47 through 50 removed outlier: 3.571A pdb=" N GLY25 48 " --> pdb=" O PHE25 56 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR25 54 " --> pdb=" O GLY25 50 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '25' and resid 62 through 67 Processing sheet with id= 43, first strand: chain '26' and resid 15 through 18 removed outlier: 5.983A pdb=" N ASN26 16 " --> pdb=" O ALA26 23 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA26 23 " --> pdb=" O ASN26 16 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER26 18 " --> pdb=" O LEU26 21 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '26' and resid 34 through 40 removed outlier: 3.698A pdb=" N HIS26 35 " --> pdb=" O LEU26 48 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '28' and resid 34 through 38 removed outlier: 3.504A pdb=" N VAL28 35 " --> pdb=" O ILE28 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE28 6 " --> pdb=" O VAL28 35 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS28 5 " --> pdb=" O GLU28 57 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N MET28 53 " --> pdb=" O THR28 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '29' and resid 11 through 15 Processing sheet with id= 47, first strand: chain '30' and resid 27 through 30 removed outlier: 6.294A pdb=" N SER30 28 " --> pdb=" O LYS30 36 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS30 36 " --> pdb=" O SER30 28 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP30 30 " --> pdb=" O GLY30 34 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '31' and resid 19 through 23 removed outlier: 6.826A pdb=" N ILE31 47 " --> pdb=" O SER31 13 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU31 35 " --> pdb=" O TYR31 48 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '33' and resid 21 through 24 removed outlier: 5.950A pdb=" N PHE33 21 " --> pdb=" O VAL33 49 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '34' and resid 13 through 18 removed outlier: 8.051A pdb=" N ASN34 13 " --> pdb=" O SER34 28 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER34 28 " --> pdb=" O ASN34 13 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'B' and resid 66 through 70 removed outlier: 3.593A pdb=" N LEU B 67 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 162 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 184 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 53 through 58 removed outlier: 3.774A pdb=" N VAL C 65 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 67 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 164 through 168 removed outlier: 3.621A pdb=" N VAL C 152 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN C 184 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP C 180 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'D' and resid 139 through 143 removed outlier: 3.670A pdb=" N ASP D 140 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP D 169 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'E' and resid 16 through 23 removed outlier: 3.726A pdb=" N ALA E 16 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 35 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE E 29 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY E 50 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'E' and resid 83 through 87 removed outlier: 3.545A pdb=" N MET E 95 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL E 93 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG E 92 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR E 127 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE E 94 " --> pdb=" O LYS E 125 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'F' and resid 34 through 37 removed outlier: 3.667A pdb=" N LYS F 35 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS F 37 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE F 6 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 64 " --> pdb=" O TYR F 4 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU F 5 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET F 9 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.827A pdb=" N ARG F 38 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN F 63 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.590A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU F 47 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'G' and resid 71 through 76 removed outlier: 7.168A pdb=" N THR G 71 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'H' and resid 22 through 28 removed outlier: 5.950A pdb=" N ALA H 22 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL H 24 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU H 59 " --> pdb=" O LYS H 49 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'H' and resid 102 through 105 removed outlier: 7.104A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'I' and resid 4 through 10 removed outlier: 3.658A pdb=" N THR I 65 " --> pdb=" O ARG I 17 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'J' and resid 44 through 52 removed outlier: 3.736A pdb=" N GLU J 47 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE J 8 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG J 7 " --> pdb=" O SER J 101 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'K' and resid 29 through 35 Processing sheet with id= 66, first strand: chain 'L' and resid 28 through 32 removed outlier: 5.242A pdb=" N LEU L 80 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG L 82 " --> pdb=" O HIS L 95 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'L' and resid 34 through 40 removed outlier: 4.802A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'P' and resid 4 through 11 removed outlier: 5.452A pdb=" N GLN P 18 " --> pdb=" O ALA P 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA P 11 " --> pdb=" O ARG P 14 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG P 14 " --> pdb=" O ALA P 11 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'P' and resid 37 through 40 removed outlier: 3.610A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Q' and resid 6 through 10 removed outlier: 3.698A pdb=" N GLY Q 9 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Q' and resid 18 through 27 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'S' and resid 46 through 51 removed outlier: 5.555A pdb=" N LEU S 46 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '03' and resid 59 through 64 removed outlier: 5.667A pdb=" N VAL03 59 " --> pdb=" O ASN03 165 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain '03' and resid 169 through 176 removed outlier: 7.199A pdb=" N GLY03 169 " --> pdb=" O LEU03 48 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR03 173 " --> pdb=" O VAL03 44 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL03 42 " --> pdb=" O ILE03 175 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER03 215 " --> pdb=" O ASP03 43 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL03 212 " --> pdb=" O VAL03 224 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Z' and resid 64 through 70 removed outlier: 3.585A pdb=" N VAL Z 67 " --> pdb=" O HIS Z 78 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY Z 15 " --> pdb=" O GLY Z 100 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE Z 102 " --> pdb=" O GLY Z 15 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE Z 17 " --> pdb=" O ILE Z 102 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR Z 129 " --> pdb=" O ASP Z 99 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE Z 131 " --> pdb=" O ALA Z 101 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Z' and resid 210 through 214 removed outlier: 5.854A pdb=" N PHE Z 210 " --> pdb=" O LYS Z 294 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLN Z 290 " --> pdb=" O ILE Z 214 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU Z 240 " --> pdb=" O CYS Z 255 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Z' and resid 216 through 219 removed outlier: 3.553A pdb=" N VAL Z 226 " --> pdb=" O PHE Z 218 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Z' and resid 335 through 341 removed outlier: 3.634A pdb=" N THR Z 335 " --> pdb=" O PHE Z 332 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE Z 332 " --> pdb=" O THR Z 335 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL Z 337 " --> pdb=" O PHE Z 330 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR Z 326 " --> pdb=" O ILE Z 341 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG Z 377 " --> pdb=" O GLN Z 329 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR Z 331 " --> pdb=" O ALA Z 375 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA Z 375 " --> pdb=" O TYR Z 331 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU Z 372 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL Z 387 " --> pdb=" O LEU Z 372 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N PHE Z 374 " --> pdb=" O ALA Z 385 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ALA Z 385 " --> pdb=" O PHE Z 374 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE Z 376 " --> pdb=" O VAL Z 383 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP Z 354 " --> pdb=" O ILE Z 310 " (cutoff:3.500A) 1764 hydrogen bonds defined for protein. 5187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3551 hydrogen bonds 5792 hydrogen bond angles 0 basepair planarities 1427 basepair parallelities 2955 stacking parallelities Total time for adding SS restraints: 290.99 Time building geometry restraints manager: 58.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 26625 1.33 - 1.46: 68980 1.46 - 1.58: 61320 1.58 - 1.71: 9613 1.71 - 1.83: 309 Bond restraints: 166847 Sorted by residual: bond pdb=" O3A GCP Z 401 " pdb=" PB GCP Z 401 " ideal model delta sigma weight residual 1.697 1.524 0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" C5 U8U Y 34 " pdb=" C6 U8U Y 34 " ideal model delta sigma weight residual 1.491 1.365 0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" O3A GCP Z 401 " pdb=" PA GCP Z 401 " ideal model delta sigma weight residual 1.621 1.516 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C1' GCP Z 401 " pdb=" N9 GCP Z 401 " ideal model delta sigma weight residual 1.463 1.559 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" N1 U8U Y 34 " pdb=" C2 U8U Y 34 " ideal model delta sigma weight residual 1.492 1.404 0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 166842 not shown) Histogram of bond angle deviations from ideal: 93.31 - 104.98: 22389 104.98 - 116.65: 126607 116.65 - 128.32: 92393 128.32 - 139.98: 7725 139.98 - 151.65: 2 Bond angle restraints: 249116 Sorted by residual: angle pdb=" N LYS11 94 " pdb=" CA LYS11 94 " pdb=" C LYS11 94 " ideal model delta sigma weight residual 113.97 100.72 13.25 1.28e+00 6.10e-01 1.07e+02 angle pdb=" N ALA10 127 " pdb=" CA ALA10 127 " pdb=" C ALA10 127 " ideal model delta sigma weight residual 113.16 100.45 12.71 1.24e+00 6.50e-01 1.05e+02 angle pdb=" N GLU10 65 " pdb=" CA GLU10 65 " pdb=" C GLU10 65 " ideal model delta sigma weight residual 113.17 100.68 12.49 1.26e+00 6.30e-01 9.83e+01 angle pdb=" N SER B 85 " pdb=" CA SER B 85 " pdb=" C SER B 85 " ideal model delta sigma weight residual 112.89 100.97 11.92 1.24e+00 6.50e-01 9.24e+01 angle pdb=" N TYR I 89 " pdb=" CA TYR I 89 " pdb=" C TYR I 89 " ideal model delta sigma weight residual 110.65 98.74 11.91 1.26e+00 6.30e-01 8.94e+01 ... (remaining 249111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 86601 35.70 - 71.41: 2580 71.41 - 107.11: 222 107.11 - 142.82: 17 142.82 - 178.52: 23 Dihedral angle restraints: 89443 sinusoidal: 71011 harmonic: 18432 Sorted by residual: dihedral pdb=" C5' C A 280 " pdb=" C4' C A 280 " pdb=" C3' C A 280 " pdb=" O3' C A 280 " ideal model delta sinusoidal sigma weight residual 147.00 74.66 72.34 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C4' C A 280 " pdb=" C3' C A 280 " pdb=" C2' C A 280 " pdb=" C1' C A 280 " ideal model delta sinusoidal sigma weight residual -35.00 33.09 -68.09 1 8.00e+00 1.56e-02 9.40e+01 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 27.18 172.82 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 89440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 27414 0.124 - 0.247: 4056 0.247 - 0.371: 293 0.371 - 0.494: 17 0.494 - 0.618: 7 Chirality restraints: 31787 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 -3.18 0.62 2.00e-01 2.50e+01 9.55e+00 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 3.02 -0.61 2.00e-01 2.50e+01 9.17e+00 chirality pdb=" C1' C011178 " pdb=" O4' C011178 " pdb=" C2' C011178 " pdb=" N1 C011178 " both_signs ideal model delta sigma weight residual False 2.47 1.86 0.61 2.00e-01 2.50e+01 9.17e+00 ... (remaining 31784 not shown) Planarity restraints: 13716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N FME W 101 " -0.242 2.00e-02 2.50e+03 1.97e-01 3.87e+02 pdb=" CA FME W 101 " 0.091 2.00e-02 2.50e+03 pdb=" CN FME W 101 " 0.271 2.00e-02 2.50e+03 pdb=" O1 FME W 101 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U011647 " -0.093 2.00e-02 2.50e+03 5.19e-02 6.06e+01 pdb=" N1 U011647 " 0.002 2.00e-02 2.50e+03 pdb=" C2 U011647 " 0.017 2.00e-02 2.50e+03 pdb=" O2 U011647 " 0.037 2.00e-02 2.50e+03 pdb=" N3 U011647 " 0.016 2.00e-02 2.50e+03 pdb=" C4 U011647 " 0.019 2.00e-02 2.50e+03 pdb=" O4 U011647 " -0.093 2.00e-02 2.50e+03 pdb=" C5 U011647 " 0.052 2.00e-02 2.50e+03 pdb=" C6 U011647 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A011328 " -0.102 2.00e-02 2.50e+03 4.40e-02 5.32e+01 pdb=" N9 A011328 " 0.010 2.00e-02 2.50e+03 pdb=" C8 A011328 " 0.042 2.00e-02 2.50e+03 pdb=" N7 A011328 " 0.033 2.00e-02 2.50e+03 pdb=" C5 A011328 " 0.018 2.00e-02 2.50e+03 pdb=" C6 A011328 " -0.015 2.00e-02 2.50e+03 pdb=" N6 A011328 " -0.067 2.00e-02 2.50e+03 pdb=" N1 A011328 " -0.006 2.00e-02 2.50e+03 pdb=" C2 A011328 " 0.019 2.00e-02 2.50e+03 pdb=" N3 A011328 " 0.036 2.00e-02 2.50e+03 pdb=" C4 A011328 " 0.033 2.00e-02 2.50e+03 ... (remaining 13713 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 1 2.03 - 2.75: 16072 2.75 - 3.47: 203391 3.47 - 4.18: 501295 4.18 - 4.90: 672278 Nonbonded interactions: 1393037 Sorted by model distance: nonbonded pdb=" O3' A Y 76 " pdb=" C LYS Y 101 " model vdw 1.318 3.270 nonbonded pdb=" O3' A Y 76 " pdb=" O LYS Y 101 " model vdw 2.257 3.040 nonbonded pdb=" O2' A Y 69 " pdb=" O5' C Y 70 " model vdw 2.277 2.440 nonbonded pdb=" C3' A Y 76 " pdb=" C LYS Y 101 " model vdw 2.346 3.700 nonbonded pdb=" N ALA10 127 " pdb=" N THR10 128 " model vdw 2.350 2.560 ... (remaining 1393032 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' and resid 1 through 76) selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4808 5.49 5 S 173 5.16 5 C 77715 2.51 5 N 28581 2.21 5 O 42503 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 5.710 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: 0.130 Extract box with map and model: 32.380 Check model and map are aligned: 1.680 Convert atoms to be neutral: 1.000 Process input model: 576.850 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 624.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 0.173 166847 Z= 0.435 Angle : 1.071 26.882 249116 Z= 0.706 Chirality : 0.090 0.618 31787 Planarity : 0.009 0.197 13716 Dihedral : 13.918 178.523 77557 Min Nonbonded Distance : 1.318 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 3.06 % Allowed : 14.31 % Favored : 82.63 % Rotamer Outliers : 1.57 % 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: -5.15 (0.08), residues: 6366 helix: -3.76 (0.07), residues: 1829 sheet: -3.26 (0.13), residues: 1059 loop : -3.33 (0.09), residues: 3478 *********************** 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 1901 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1818 time to evaluate : 6.787 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: 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 22 residues processed: 1878 average time/residue: 1.4959 time to fit residues: 4707.3003 Evaluate side-chains 1037 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1015 time to evaluate : 8.918 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 1.5910 time to fit residues: 69.2197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 929 optimal weight: 20.0000 chunk 834 optimal weight: 20.0000 chunk 463 optimal weight: 6.9990 chunk 285 optimal weight: 8.9990 chunk 562 optimal weight: 9.9990 chunk 445 optimal weight: 5.9990 chunk 862 optimal weight: 20.0000 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: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 36 ASN 04 44 ASN 04 127 ASN 04 225 ASN 04 259 ASN ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 94 GLN 06 165 HIS 07 126 ASN ** 08 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 142 GLN 09 33 GLN 09 119 ASN 09 135 HIS 10 103 ASN ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 131 ASN 13 5 GLN 13 29 HIS 13 88 ASN 14 4 ASN ** 14 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 13 HIS 15 17 ASN 16 9 GLN ** 16 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 23 ASN 17 19 GLN 18 6 GLN 18 14 GLN ** 18 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 65 ASN ** 19 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 86 GLN ** 20 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 21 15 GLN ** 21 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 68 ASN 23 73 ASN 24 49 ASN ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN 24 87 GLN ** 25 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 26 15 ASN 26 19 HIS 27 58 ASN 28 19 HIS 29 20 ASN 29 61 ASN 34 35 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS B 176 ASN B 177 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 125 ASN D 130 ASN D 135 GLN E 18 ASN F 55 HIS ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN G 147 ASN H 20 ASN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 39 ASN L 4 ASN ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 45 ASN ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 HIS P 79 ASN Q 30 HIS R 51 GLN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 ASN 03 20 GLN 03 24 ASN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 HIS ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 290 GLN ** Z 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.123 166847 Z= 0.338 Angle : 0.803 16.509 249116 Z= 0.416 Chirality : 0.044 0.446 31787 Planarity : 0.007 0.158 13716 Dihedral : 14.074 178.374 64894 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 25.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.95 % Favored : 87.68 % Rotamer Outliers : 5.26 % 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: -3.85 (0.09), residues: 6366 helix: -2.09 (0.10), residues: 1917 sheet: -2.86 (0.14), residues: 1077 loop : -2.75 (0.10), residues: 3372 *********************** 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 1419 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1141 time to evaluate : 6.847 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 outliers start: 278 outliers final: 159 residues processed: 1296 average time/residue: 1.5352 time to fit residues: 3486.9127 Evaluate side-chains 1073 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 914 time to evaluate : 7.321 Switching outliers to nearest non-outliers outliers start: 159 outliers final: 0 residues processed: 159 average time/residue: 1.2264 time to fit residues: 377.6994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 555 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 832 optimal weight: 20.0000 chunk 680 optimal weight: 20.0000 chunk 275 optimal weight: 30.0000 chunk 1001 optimal weight: 20.0000 chunk 1082 optimal weight: 50.0000 chunk 892 optimal weight: 30.0000 chunk 993 optimal weight: 20.0000 chunk 341 optimal weight: 20.0000 chunk 803 optimal weight: 20.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 44 ASN ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 134 HIS 05 150 GLN ** 06 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 07 126 ASN 08 19 ASN ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 09 133 GLN 10 9 GLN ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN 14 4 ASN 14 104 GLN 15 17 ASN 18 40 GLN 19 51 GLN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 65 GLN 23 98 ASN ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 25 72 ASN 27 20 ASN ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 34 13 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN L 45 ASN O 49 HIS ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 301 HIS Z 355 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.133 166847 Z= 0.394 Angle : 0.824 15.258 249116 Z= 0.423 Chirality : 0.044 0.394 31787 Planarity : 0.007 0.149 13716 Dihedral : 14.996 178.569 64894 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 31.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.29 % Favored : 85.42 % Rotamer Outliers : 5.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.59 (0.10), residues: 6366 helix: -1.74 (0.10), residues: 1944 sheet: -2.65 (0.14), residues: 1027 loop : -2.72 (0.10), residues: 3395 *********************** 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 1249 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 982 time to evaluate : 6.606 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 outliers start: 267 outliers final: 136 residues processed: 1163 average time/residue: 1.4771 time to fit residues: 3047.3120 Evaluate side-chains 970 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 834 time to evaluate : 6.696 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 0 residues processed: 136 average time/residue: 1.2371 time to fit residues: 329.4633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 110 optimal weight: 20.0000 chunk 478 optimal weight: 0.0870 chunk 672 optimal weight: 20.0000 chunk 1005 optimal weight: 20.0000 chunk 1064 optimal weight: 40.0000 chunk 525 optimal weight: 20.0000 chunk 952 optimal weight: 30.0000 chunk 286 optimal weight: 5.9990 overall best weight: 10.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 126 ASN ** 05 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 103 ASN 08 114 HIS 08 142 GLN ** 09 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 11 GLN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 131 ASN 13 3 GLN 15 17 ASN 15 88 ASN ** 19 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 82 HIS ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 98 ASN ** 24 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN ** 25 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 26 19 HIS ** 27 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 32 6 GLN ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 119 GLN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 ASN O 61 GLN ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.129 166847 Z= 0.315 Angle : 0.734 14.269 249116 Z= 0.378 Chirality : 0.040 0.415 31787 Planarity : 0.006 0.143 13716 Dihedral : 15.136 176.212 64894 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.22 % Favored : 87.56 % Rotamer Outliers : 4.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.08 % 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: -3.29 (0.10), residues: 6366 helix: -1.39 (0.11), residues: 1938 sheet: -2.57 (0.14), residues: 1061 loop : -2.56 (0.10), residues: 3367 *********************** 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 1153 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 935 time to evaluate : 6.627 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 outliers start: 218 outliers final: 124 residues processed: 1065 average time/residue: 1.3811 time to fit residues: 2592.3591 Evaluate side-chains 948 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 824 time to evaluate : 6.787 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 0 residues processed: 124 average time/residue: 1.1653 time to fit residues: 280.3810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 792 optimal weight: 30.0000 chunk 439 optimal weight: 10.0000 chunk 908 optimal weight: 20.0000 chunk 735 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 543 optimal weight: 9.9990 chunk 955 optimal weight: 50.0000 chunk 268 optimal weight: 50.0000 overall best weight: 12.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 94 GLN ** 08 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 08 142 GLN ** 09 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 9 GLN ** 12 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 89 ASN ** 14 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 17 ASN ** 19 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 20 ASN 27 31 GLN ** 27 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** 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 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.121 166847 Z= 0.381 Angle : 0.806 15.352 249116 Z= 0.412 Chirality : 0.043 0.385 31787 Planarity : 0.006 0.102 13716 Dihedral : 15.675 178.638 64894 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 34.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.39 % Favored : 85.41 % Rotamer Outliers : 4.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.08 % 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: -3.31 (0.10), residues: 6366 helix: -1.43 (0.11), residues: 1955 sheet: -2.53 (0.14), residues: 1040 loop : -2.59 (0.10), residues: 3371 *********************** 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 1081 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 866 time to evaluate : 6.841 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 outliers start: 215 outliers final: 121 residues processed: 1001 average time/residue: 1.3902 time to fit residues: 2462.7709 Evaluate side-chains 904 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 783 time to evaluate : 6.790 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 0 residues processed: 121 average time/residue: 1.1689 time to fit residues: 277.3495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 358 optimal weight: 6.9990 chunk 958 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 624 optimal weight: 30.0000 chunk 262 optimal weight: 20.0000 chunk 1065 optimal weight: 7.9990 chunk 884 optimal weight: 30.0000 chunk 493 optimal weight: 30.0000 chunk 88 optimal weight: 0.7980 chunk 352 optimal weight: 10.0000 chunk 559 optimal weight: 0.9980 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 85 ASN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 29 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN 08 142 GLN 09 133 GLN 12 131 ASN ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 17 ASN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 88 HIS 26 16 ASN ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 ASN O 61 GLN O 79 GLN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS Z 90 ASN ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.151 166847 Z= 0.202 Angle : 0.665 19.297 249116 Z= 0.341 Chirality : 0.036 0.377 31787 Planarity : 0.005 0.155 13716 Dihedral : 15.339 176.270 64894 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.29 % Favored : 89.51 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -2.87 (0.10), residues: 6366 helix: -0.95 (0.11), residues: 1942 sheet: -2.35 (0.15), residues: 1051 loop : -2.36 (0.10), residues: 3373 *********************** 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 1053 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 931 time to evaluate : 6.782 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 outliers start: 122 outliers final: 64 residues processed: 1006 average time/residue: 1.3451 time to fit residues: 2390.5117 Evaluate side-chains 887 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 823 time to evaluate : 6.771 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 1.1248 time to fit residues: 143.3701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 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: 10.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 49 GLN ** 05 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 08 142 GLN ** 09 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 89 ASN 15 17 ASN ** 15 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 30 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** 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** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.159 166847 Z= 0.559 Angle : 0.961 13.167 249116 Z= 0.483 Chirality : 0.049 0.481 31787 Planarity : 0.007 0.148 13716 Dihedral : 16.251 178.426 64894 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 42.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 15.19 % Favored : 84.53 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.08 % 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: -3.48 (0.10), residues: 6366 helix: -1.59 (0.11), residues: 1952 sheet: -2.51 (0.14), residues: 1066 loop : -2.73 (0.10), residues: 3348 *********************** 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 987 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 801 time to evaluate : 6.829 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 outliers start: 186 outliers final: 118 residues processed: 914 average time/residue: 1.3624 time to fit residues: 2196.6838 Evaluate side-chains 875 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 757 time to evaluate : 6.805 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 0 residues processed: 118 average time/residue: 1.1468 time to fit residues: 263.3970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 633 optimal weight: 20.0000 chunk 319 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 674 optimal weight: 20.0000 chunk 722 optimal weight: 5.9990 chunk 524 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 834 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 136 GLN ** 07 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 09 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 66 ASN ** 09 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 133 GLN ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 17 ASN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 31 44 GLN ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** 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 36 GLN I 49 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN K 21 HIS ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN O 61 GLN R 30 ASN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.160 166847 Z= 0.249 Angle : 0.710 15.263 249116 Z= 0.364 Chirality : 0.038 0.509 31787 Planarity : 0.006 0.122 13716 Dihedral : 15.851 177.522 64894 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 28.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.47 % Favored : 88.36 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -3.07 (0.10), residues: 6366 helix: -1.19 (0.11), residues: 1946 sheet: -2.37 (0.15), residues: 1079 loop : -2.47 (0.10), residues: 3341 *********************** 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 935 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 871 time to evaluate : 6.169 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 outliers start: 64 outliers final: 32 residues processed: 906 average time/residue: 1.3589 time to fit residues: 2174.6082 Evaluate side-chains 850 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 818 time to evaluate : 6.850 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 1.2732 time to fit residues: 81.8027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 927 optimal weight: 20.0000 chunk 988 optimal weight: 20.0000 chunk 595 optimal weight: 20.0000 chunk 430 optimal weight: 3.9990 chunk 776 optimal weight: 20.0000 chunk 303 optimal weight: 10.0000 chunk 893 optimal weight: 30.0000 chunk 935 optimal weight: 30.0000 chunk 985 optimal weight: 20.0000 overall best weight: 14.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 89 ASN ** 13 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN ** 25 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 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** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.175 166847 Z= 0.429 Angle : 0.851 13.957 249116 Z= 0.433 Chirality : 0.044 0.373 31787 Planarity : 0.007 0.159 13716 Dihedral : 16.344 179.233 64894 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 38.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.91 % Favored : 84.92 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -3.39 (0.10), residues: 6366 helix: -1.49 (0.11), residues: 1966 sheet: -2.48 (0.15), residues: 1060 loop : -2.67 (0.10), residues: 3340 *********************** 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 908 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 794 time to evaluate : 6.805 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 outliers start: 114 outliers final: 81 residues processed: 851 average time/residue: 1.4156 time to fit residues: 2137.9033 Evaluate side-chains 843 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 762 time to evaluate : 6.840 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 1.1532 time to fit residues: 186.0048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 40.0000 chunk 638 optimal weight: 20.0000 chunk 496 optimal weight: 7.9990 chunk 726 optimal weight: 20.0000 chunk 1096 optimal weight: 8.9990 chunk 1009 optimal weight: 20.0000 chunk 873 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 674 optimal weight: 20.0000 chunk 535 optimal weight: 10.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 14 HIS ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 60 GLN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 80 ASN ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 51 GLN 24 75 GLN ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 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** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.194 166847 Z= 0.385 Angle : 0.812 15.837 249116 Z= 0.414 Chirality : 0.043 0.511 31787 Planarity : 0.006 0.135 13716 Dihedral : 16.416 179.677 64894 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 35.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.76 % Favored : 86.07 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.08 % 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: -3.40 (0.10), residues: 6366 helix: -1.52 (0.11), residues: 1957 sheet: -2.52 (0.15), residues: 1077 loop : -2.64 (0.10), residues: 3332 ********************** 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 839 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 801 time to evaluate : 6.804 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 outliers start: 38 outliers final: 22 residues processed: 822 average time/residue: 1.3584 time to fit residues: 1968.4877 Evaluate side-chains 785 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 763 time to evaluate : 8.714 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 1.1009 time to fit residues: 52.6580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 693 optimal weight: 20.0000 chunk 930 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 805 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 242 optimal weight: 6.9990 chunk 874 optimal weight: 20.0000 chunk 366 optimal weight: 7.9990 chunk 898 optimal weight: 30.0000 chunk 110 optimal weight: 30.0000 chunk 161 optimal weight: 30.0000 overall best weight: 12.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 14 HIS ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 89 ASN ** 13 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN ** 25 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 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** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.041867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.035829 restraints weight = 1545531.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.036808 restraints weight = 629980.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.037373 restraints weight = 344511.548| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.189 166847 Z= 0.383 Angle : 0.816 17.491 249116 Z= 0.416 Chirality : 0.043 0.355 31787 Planarity : 0.006 0.124 13716 Dihedral : 16.536 179.799 64894 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 36.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.61 % Favored : 85.17 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.08 % 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: -3.39 (0.10), residues: 6366 helix: -1.52 (0.11), residues: 1972 sheet: -2.53 (0.15), residues: 1056 loop : -2.63 (0.10), residues: 3338 =============================================================================== Job complete usr+sys time: 38759.18 seconds wall clock time: 672 minutes 34.16 seconds (40354.16 seconds total)