Starting phenix.real_space_refine (version: dev) on Tue May 24 11:22:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/05_2022/5uyq_8620_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/05_2022/5uyq_8620.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/05_2022/5uyq_8620_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/05_2022/5uyq_8620_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/05_2022/5uyq_8620_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/05_2022/5uyq_8620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/05_2022/5uyq_8620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/05_2022/5uyq_8620_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/05_2022/5uyq_8620_updated.pdb" } resolution = 3.8 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= -0.340 sd= 1.063 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 "10 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "12 ARG 13": "NH1" <-> "NH2" Residue "12 ARG 37": "NH1" <-> "NH2" Residue "12 ARG 96": "NH1" <-> "NH2" Residue "12 ARG 120": "NH1" <-> "NH2" Residue "14 ARG 21": "NH1" <-> "NH2" Residue "14 ARG 33": "NH1" <-> "NH2" Residue "14 ARG 41": "NH1" <-> "NH2" Residue "14 ARG 47": "NH1" <-> "NH2" Residue "14 ARG 60": "NH1" <-> "NH2" Residue "14 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 ARG 78": "NH1" <-> "NH2" Residue "14 ARG 126": "NH1" <-> "NH2" Residue "15 ARG 10": "NH1" <-> "NH2" Residue "15 ARG 18": "NH1" <-> "NH2" Residue "15 ARG 40": "NH1" <-> "NH2" Residue "15 ARG 44": "NH1" <-> "NH2" Residue "15 ARG 50": "NH1" <-> "NH2" Residue "15 ARG 55": "NH1" <-> "NH2" Residue "15 ARG 59": "NH1" <-> "NH2" Residue "15 ARG 114": "NH1" <-> "NH2" Residue "16 ARG 8": "NH1" <-> "NH2" Residue "16 ARG 12": "NH1" <-> "NH2" Residue "16 ARG 17": "NH1" <-> "NH2" Residue "16 ARG 22": "NH1" <-> "NH2" Residue "16 ARG 46": "NH1" <-> "NH2" Residue "16 ARG 63": "NH1" <-> "NH2" Residue "16 ARG 64": "NH1" <-> "NH2" Residue "16 ARG 69": "NH1" <-> "NH2" Residue "16 ARG 71": "NH1" <-> "NH2" Residue "16 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 "20 PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "24 TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "27 ARG 29": "NH1" <-> "NH2" Residue "27 ARG 47": "NH1" <-> "NH2" Residue "27 ARG 52": "NH1" <-> "NH2" Residue "28 ARG 10": "NH1" <-> "NH2" Residue "28 ARG 29": "NH1" <-> "NH2" Residue "28 ARG 44": "NH1" <-> "NH2" Residue "29 ARG 49": "NH1" <-> "NH2" Residue "29 ARG 56": "NH1" <-> "NH2" Residue "30 ARG 9": "NH1" <-> "NH2" Residue "30 ARG 15": "NH1" <-> "NH2" Residue "30 ARG 39": "NH1" <-> "NH2" Residue "30 ARG 51": "NH1" <-> "NH2" Residue "31 ARG 43": "NH1" <-> "NH2" Residue "32 ARG 3": "NH1" <-> "NH2" Residue "32 ARG 12": "NH1" <-> "NH2" Residue "32 ARG 14": "NH1" <-> "NH2" Residue "32 ARG 19": "NH1" <-> "NH2" Residue "32 ARG 21": "NH1" <-> "NH2" Residue "32 ARG 33": "NH1" <-> "NH2" Residue "32 ARG 41": "NH1" <-> "NH2" Residue "33 ARG 12": "NH1" <-> "NH2" Residue "33 ARG 29": "NH1" <-> "NH2" Residue "33 ARG 39": "NH1" <-> "NH2" Residue "33 ARG 41": "NH1" <-> "NH2" Residue "34 ARG 12": "NH1" <-> "NH2" Residue "34 ARG 24": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "03 ARG 7": "NH1" <-> "NH2" Residue "03 ARG 12": "NH1" <-> "NH2" Residue "03 ARG 162": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 153759 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': 91, 'rna3p_pur': 783, 'rna2p_pyr': 47, 'rna3p_pyr': 618} Link IDs: {'rna3p': 1400, 'rna2p': 138} 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': 213, 'rna3p_pur': 1461, 'rna2p_pyr': 97, 'rna3p_pyr': 1132} Link IDs: {'rna3p': 2592, 'rna2p': 310} 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: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 395 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 15, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 15, 'rna2p': 2} 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: {'rna3p': 1, 'rna2p_pyr': 7, 'p5*END': 1, 'rna3p_pur': 29, 'rna3p_pyr': 31, 'rna2p_pur': 8} Link IDs: {'rna3p': 61, 'rna2p': 14} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GCP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 60.67, per 1000 atoms: 0.39 Number of scatterers: 153759 At special positions: 0 Unit cell: (277.16, 265.68, 238.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 173 16.00 P 4807 15.00 Mg 1 11.99 O 42497 8.00 N 28576 7.00 C 77705 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: 54.36 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: 194 helices and 79 sheets defined 37.9% alpha, 18.6% beta 1394 base pairs and 2878 stacking pairs defined. Time for finding SS restraints: 66.83 Creating SS restraints... Processing helix chain '04' and resid 10 through 15 removed outlier: 7.720A pdb=" N HIS04 14 " --> pdb=" O PRO04 10 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL04 15 " --> pdb=" O GLY04 11 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 10 through 15' Processing helix chain '04' and resid 29 through 34 removed outlier: 4.010A pdb=" N LEU04 33 " --> pdb=" O PHE04 29 " (cutoff:3.500A) removed outlier: 5.646A 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 206 through 214 removed outlier: 4.179A pdb=" N ALA04 210 " --> pdb=" O LYS04 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG04 213 " --> pdb=" O ALA04 209 " (cutoff:3.500A) Processing helix chain '04' and resid 220 through 225 removed outlier: 5.535A pdb=" N ASN04 225 " --> pdb=" O GLY04 221 " (cutoff:3.500A) Processing helix chain '04' and resid 259 through 267 removed outlier: 6.090A pdb=" N ASP04 263 " --> pdb=" O ASN04 259 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LYS04 264 " --> pdb=" O LYS04 260 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE04 265 " --> pdb=" O ARG04 261 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE04 266 " --> pdb=" O THR04 262 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL04 267 " --> pdb=" O ASP04 263 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 259 through 267' Processing helix chain '05' and resid 61 through 72 Processing helix chain '05' and resid 98 through 105 removed outlier: 4.065A pdb=" N ALA05 102 " --> pdb=" O VAL05 98 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP05 103 " --> pdb=" O GLU05 99 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL05 104 " --> pdb=" O LEU05 100 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYS05 105 " --> pdb=" O PHE05 101 " (cutoff:3.500A) No H-bonds generated for 'chain '05' and resid 98 through 105' Processing helix chain '05' and resid 120 through 126 removed outlier: 4.613A pdb=" N TRP05 125 " --> pdb=" O GLY05 120 " (cutoff:3.500A) Processing helix chain '06' and resid 24 through 41 removed outlier: 3.577A pdb=" N ALA06 39 " --> pdb=" O TYR06 35 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLN06 41 " --> pdb=" O ALA06 37 " (cutoff:3.500A) Processing helix chain '06' and resid 48 through 53 removed outlier: 7.754A pdb=" N THR06 53 " --> pdb=" O ARG06 49 " (cutoff:3.500A) Processing helix chain '06' and resid 97 through 116 Processing helix chain '06' and resid 130 through 142 removed outlier: 3.540A pdb=" N LEU06 134 " --> pdb=" O LYS06 130 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA06 142 " --> pdb=" O LEU06 138 " (cutoff:3.500A) Processing helix chain '06' and resid 155 through 163 removed outlier: 3.973A pdb=" N ALA06 160 " --> pdb=" O ASN06 156 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN06 163 " --> pdb=" O LEU06 159 " (cutoff:3.500A) Processing helix chain '06' and resid 176 through 184 removed outlier: 3.518A pdb=" N ILE06 181 " --> pdb=" O PRO06 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE06 183 " --> pdb=" O SER06 179 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASP06 184 " --> pdb=" O LEU06 180 " (cutoff:3.500A) Processing helix chain '06' and resid 189 through 201 removed outlier: 3.938A pdb=" N LYS06 194 " --> pdb=" O ALA06 190 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN06 195 " --> pdb=" O ASP06 191 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET06 199 " --> pdb=" O GLN06 195 " (cutoff:3.500A) Processing helix chain '06' and resid 15 through 20 removed outlier: 3.997A pdb=" N GLY06 20 " --> pdb=" O SER06 15 " (cutoff:3.500A) No H-bonds generated for 'chain '06' and resid 15 through 20' Processing helix chain '07' and resid 1 through 20 removed outlier: 3.562A pdb=" N ASP07 5 " --> pdb=" O ALA07 1 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL07 12 " --> pdb=" O LYS07 8 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS07 13 " --> pdb=" O ASP07 9 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU07 18 " --> pdb=" O LYS07 14 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN07 20 " --> pdb=" O MET07 16 " (cutoff:3.500A) Processing helix chain '07' and resid 41 through 46 removed outlier: 3.748A pdb=" N ASP07 45 " --> pdb=" O GLU07 41 " (cutoff:3.500A) removed outlier: 4.562A 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 60 removed outlier: 3.623A pdb=" N LEU07 56 " --> pdb=" O ALA07 52 " (cutoff:3.500A) Processing helix chain '07' and resid 92 through 110 removed outlier: 3.838A pdb=" N TRP07 96 " --> pdb=" O GLY07 92 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE07 105 " --> pdb=" O ARG07 101 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL07 107 " --> pdb=" O ILE07 103 " (cutoff:3.500A) Proline residue: 07 108 - end of helix Processing helix chain '07' and resid 161 through 173 removed outlier: 3.689A pdb=" N ALA07 167 " --> pdb=" O GLU07 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA07 171 " --> pdb=" O ALA07 167 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE07 172 " --> pdb=" O LEU07 168 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP07 173 " --> pdb=" O LEU07 169 " (cutoff:3.500A) Processing helix chain '07' and resid 133 through 138 removed outlier: 3.738A pdb=" N ILE07 136 " --> pdb=" O GLU07 133 " (cutoff:3.500A) Proline residue: 07 138 - end of helix Processing helix chain '08' and resid 1 through 7 removed outlier: 4.555A pdb=" N ALA08 6 " --> pdb=" O ARG08 2 " (cutoff:3.500A) Proline residue: 08 7 - end of helix Processing helix chain '08' and resid 59 through 80 Processing helix chain '08' and resid 136 through 152 removed outlier: 4.041A pdb=" N ILE08 140 " --> pdb=" O ASP08 136 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR08 150 " --> pdb=" O ASP08 146 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG08 151 " --> pdb=" O LEU08 147 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG08 152 " --> pdb=" O ARG08 148 " (cutoff:3.500A) Processing helix chain '09' and resid 22 through 28 Processing helix chain '09' and resid 29 through 34 Processing helix chain '09' and resid 40 through 50 removed outlier: 3.970A pdb=" N ARG09 50 " --> pdb=" O PHE09 46 " (cutoff:3.500A) Processing helix chain '09' and resid 51 through 73 removed outlier: 4.444A pdb=" N ALA09 56 " --> pdb=" O ALA09 52 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS09 57 " --> pdb=" O GLU09 53 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU09 60 " --> pdb=" O ALA09 56 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL09 61 " --> pdb=" O LYS09 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU09 62 " --> pdb=" O LEU09 58 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA09 63 " --> pdb=" O ALA09 59 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA09 64 " --> pdb=" O GLU09 60 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASN09 73 " --> pdb=" O ALA09 69 " (cutoff:3.500A) Processing helix chain '09' and resid 95 through 107 removed outlier: 3.606A pdb=" N ILE09 99 " --> pdb=" O GLY09 95 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR09 104 " --> pdb=" O ALA09 100 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA09 105 " --> pdb=" O ASP09 101 " (cutoff:3.500A) Processing helix chain '10' and resid 3 through 21 removed outlier: 3.712A pdb=" N ILE10 11 " --> pdb=" O ASP10 7 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU10 14 " --> pdb=" O ALA10 10 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU10 17 " --> pdb=" O ALA10 13 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA10 19 " --> pdb=" O VAL10 15 " (cutoff:3.500A) Processing helix chain '10' and resid 33 through 48 removed outlier: 3.680A pdb=" N THR10 39 " --> pdb=" O VAL10 35 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG10 42 " --> pdb=" O MET10 38 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA10 44 " --> pdb=" O GLU10 40 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU10 47 " --> pdb=" O LYS10 43 " (cutoff:3.500A) Processing helix chain '10' and resid 62 through 71 removed outlier: 3.757A pdb=" N GLY10 66 " --> pdb=" O ARG10 62 " (cutoff:3.500A) Proline residue: 10 68 - end of helix removed outlier: 4.339A pdb=" N CYS10 71 " --> pdb=" O THR10 67 " (cutoff:3.500A) Processing helix chain '10' and resid 74 through 79 removed outlier: 4.534A pdb=" N GLY10 78 " --> pdb=" O ASP10 74 " (cutoff:3.500A) Proline residue: 10 79 - end of helix No H-bonds generated for 'chain '10' and resid 74 through 79' Processing helix chain '10' and resid 94 through 106 removed outlier: 3.913A pdb=" N GLU10 98 " --> pdb=" O ARG10 94 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE10 99 " --> pdb=" O LEU10 95 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA10 100 " --> pdb=" O PHE10 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS10 101 " --> pdb=" O LYS10 97 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN10 103 " --> pdb=" O PHE10 99 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA10 104 " --> pdb=" O ALA10 100 " (cutoff:3.500A) Processing helix chain '10' and resid 109 through 114 removed outlier: 6.138A pdb=" N ALA10 112 " --> pdb=" O LYS10 109 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU10 114 " --> pdb=" O ALA10 111 " (cutoff:3.500A) Processing helix chain '11' and resid 23 through 31 removed outlier: 4.578A pdb=" N LEU11 27 " --> pdb=" O VAL11 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY11 28 " --> pdb=" O GLY11 24 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN11 30 " --> pdb=" O ALA11 26 " (cutoff:3.500A) Processing helix chain '11' and resid 33 through 48 removed outlier: 3.640A pdb=" N LYS11 39 " --> pdb=" O MET11 35 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN11 42 " --> pdb=" O CYS11 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA11 43 " --> pdb=" O LYS11 39 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS11 44 " --> pdb=" O ALA11 40 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP11 46 " --> pdb=" O ASN11 42 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER11 47 " --> pdb=" O ALA11 43 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE11 48 " --> pdb=" O LYS11 44 " (cutoff:3.500A) Processing helix chain '11' and resid 74 through 82 removed outlier: 3.771A pdb=" N LYS11 80 " --> pdb=" O ALA11 76 " (cutoff:3.500A) Processing helix chain '11' and resid 103 through 113 removed outlier: 3.977A pdb=" N GLU11 107 " --> pdb=" O ALA11 103 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE11 108 " --> pdb=" O GLN11 104 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR11 111 " --> pdb=" O GLU11 107 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS11 112 " --> pdb=" O ILE11 108 " (cutoff:3.500A) Processing helix chain '11' and resid 120 through 136 removed outlier: 3.684A pdb=" N GLY11 136 " --> pdb=" O ALA11 132 " (cutoff:3.500A) Processing helix chain '12' and resid 24 through 38 removed outlier: 3.773A pdb=" N GLU12 31 " --> pdb=" O ARG12 27 " (cutoff:3.500A) Processing helix chain '12' and resid 88 through 96 Processing helix chain '12' and resid 97 through 110 removed outlier: 4.522A pdb=" N ILE12 101 " --> pdb=" O PRO12 97 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU12 102 " --> pdb=" O GLU12 98 " (cutoff:3.500A) Proline residue: 12 110 - end of helix Processing helix chain '12' and resid 112 through 122 removed outlier: 4.998A pdb=" N LYS12 121 " --> pdb=" O ALA12 117 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU12 122 " --> pdb=" O MET12 118 " (cutoff:3.500A) Processing helix chain '13' and resid 109 through 120 removed outlier: 6.451A pdb=" N MET13 113 " --> pdb=" O SER13 109 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS13 114 " --> pdb=" O GLU13 110 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE13 115 " --> pdb=" O LYS13 111 " (cutoff:3.500A) Proline residue: 13 120 - end of helix 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: 4.092A pdb=" N ALA14 72 " --> pdb=" O SER14 68 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE14 73 " --> pdb=" O ARG14 69 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR14 74 " --> pdb=" O LYS14 70 " (cutoff:3.500A) removed outlier: 6.907A 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 85 removed outlier: 3.553A pdb=" N LEU14 82 " --> pdb=" O ARG14 78 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA14 83 " --> pdb=" O LEU14 79 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS14 84 " --> pdb=" O SER14 80 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL14 85 " --> pdb=" O ASP14 81 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 78 through 85' Processing helix chain '14' and resid 93 through 99 removed outlier: 5.523A pdb=" N ALA14 97 " --> pdb=" O ASN14 93 " (cutoff:3.500A) Processing helix chain '14' and resid 128 through 139 removed outlier: 3.589A pdb=" N ALA14 133 " --> pdb=" O LYS14 129 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA14 134 " --> pdb=" O GLY14 130 " (cutoff:3.500A) Processing helix chain '15' and resid 42 through 58 removed outlier: 3.585A pdb=" N ILE15 46 " --> pdb=" O THR15 42 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA15 52 " --> pdb=" O ALA15 48 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA15 56 " --> pdb=" O ALA15 52 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL15 57 " --> pdb=" O MET15 53 " (cutoff:3.500A) Processing helix chain '15' and resid 109 through 125 removed outlier: 3.649A pdb=" N LYS15 118 " --> pdb=" O ARG15 114 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA15 122 " --> pdb=" O LYS15 118 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS15 123 " --> pdb=" O LEU15 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU15 124 " --> pdb=" O ALA15 120 " (cutoff:3.500A) Proline residue: 15 125 - end of helix Processing helix chain '16' and resid 13 through 32 removed outlier: 3.716A pdb=" N PHE16 21 " --> pdb=" O ARG16 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN16 23 " --> pdb=" O ALA16 19 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG16 30 " --> pdb=" O GLY16 26 " (cutoff:3.500A) Processing helix chain '16' and resid 37 through 58 removed outlier: 3.681A pdb=" N GLU16 43 " --> pdb=" O PRO16 39 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG16 45 " --> pdb=" O ALA16 41 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG16 46 " --> pdb=" O LYS16 42 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL16 47 " --> pdb=" O GLU16 43 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU16 49 " --> pdb=" O ARG16 45 " (cutoff:3.500A) Proline residue: 16 50 - end of helix removed outlier: 3.689A pdb=" N LYS16 56 " --> pdb=" O ILE16 52 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR16 57 " --> pdb=" O THR16 53 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASP16 58 " --> pdb=" O LEU16 54 " (cutoff:3.500A) Processing helix chain '16' and resid 59 through 71 removed outlier: 4.845A pdb=" N THR16 70 " --> pdb=" O ALA16 66 " (cutoff:3.500A) Processing helix chain '16' and resid 72 through 88 removed outlier: 4.448A pdb=" N PHE16 80 " --> pdb=" O VAL16 76 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN16 81 " --> pdb=" O ALA16 77 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU16 83 " --> pdb=" O LEU16 79 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY16 84 " --> pdb=" O PHE16 80 " (cutoff:3.500A) Proline residue: 16 85 - end of helix Processing helix chain '17' and resid 2 through 20 removed outlier: 3.676A pdb=" N ARG17 10 " --> pdb=" O ALA17 6 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG17 13 " --> pdb=" O ARG17 9 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA17 14 " --> pdb=" O ARG17 10 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU17 18 " --> pdb=" O ALA17 14 " (cutoff:3.500A) Processing helix chain '17' and resid 58 through 63 removed outlier: 4.381A pdb=" N LYS17 63 " --> pdb=" O ALA17 59 " (cutoff:3.500A) Processing helix chain '17' and resid 67 through 86 removed outlier: 3.674A pdb=" N ARG17 81 " --> pdb=" O ALA17 77 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU17 83 " --> pdb=" O ALA17 79 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU17 84 " --> pdb=" O GLU17 80 " (cutoff:3.500A) Processing helix chain '17' and resid 101 through 114 Processing helix chain '18' and resid 1 through 13 removed outlier: 3.696A pdb=" N GLU18 10 " --> pdb=" O GLN18 6 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN18 11 " --> pdb=" O LEU18 7 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS18 13 " --> pdb=" O GLN18 9 " (cutoff:3.500A) Processing helix chain '18' and resid 96 through 103 removed outlier: 4.599A pdb=" N ARG18 100 " --> pdb=" O LEU18 96 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU18 101 " --> pdb=" O TYR18 97 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG18 102 " --> pdb=" O TYR18 98 " (cutoff:3.500A) removed outlier: 5.836A 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 6 through 21 removed outlier: 3.643A pdb=" N ILE19 16 " --> pdb=" O ARG19 12 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN19 19 " --> pdb=" O LYS19 15 " (cutoff:3.500A) Processing helix chain '19' and resid 25 through 30 removed outlier: 3.710A pdb=" N ARG19 29 " --> pdb=" O GLY19 25 " (cutoff:3.500A) Processing helix chain '19' and resid 31 through 36 removed outlier: 4.187A pdb=" N GLN19 36 " --> pdb=" O ARG19 32 " (cutoff:3.500A) Processing helix chain '19' and resid 38 through 60 removed outlier: 3.628A pdb=" N ARG19 47 " --> pdb=" O GLN19 43 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG19 50 " --> pdb=" O TYR19 46 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS19 53 " --> pdb=" O ARG19 49 " (cutoff:3.500A) removed outlier: 3.927A 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 removed outlier: 3.666A pdb=" N ASN19 80 " --> pdb=" O SER19 76 " (cutoff:3.500A) Processing helix chain '19' and resid 90 through 101 removed outlier: 4.395A pdb=" N ASP19 96 " --> pdb=" O LYS19 92 " (cutoff:3.500A) Processing helix chain '19' and resid 102 through 117 removed outlier: 3.678A pdb=" N ALA19 107 " --> pdb=" O VAL19 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA19 117 " --> pdb=" O LYS19 113 " (cutoff:3.500A) Processing helix chain '21' and resid 13 through 23 removed outlier: 3.682A pdb=" N ARG21 18 " --> pdb=" O ALA21 14 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL21 20 " --> pdb=" O LYS21 16 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU21 23 " --> pdb=" O LEU21 19 " (cutoff:3.500A) Processing helix chain '21' and resid 28 through 39 Processing helix chain '21' and resid 41 through 61 removed outlier: 3.555A pdb=" N VAL21 45 " --> pdb=" O LYS21 41 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL21 50 " --> pdb=" O LEU21 46 " (cutoff:3.500A) Processing helix chain '22' and resid 1 through 11 removed outlier: 4.018A pdb=" N GLU22 5 " --> pdb=" O MET22 1 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU22 8 " --> pdb=" O GLU22 4 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS22 9 " --> pdb=" O GLU22 5 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU22 11 " --> pdb=" O LEU22 7 " (cutoff:3.500A) Processing helix chain '22' and resid 17 through 26 removed outlier: 3.509A pdb=" N SER22 21 " --> pdb=" O SER22 17 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR22 22 " --> pdb=" O GLU22 18 " (cutoff:3.500A) Processing helix chain '22' and resid 39 through 50 removed outlier: 3.521A pdb=" N LYS22 44 " --> pdb=" O LYS22 40 " (cutoff:3.500A) Processing helix chain '23' and resid 65 through 70 removed outlier: 4.098A pdb=" N VAL23 69 " --> pdb=" O GLN23 65 " (cutoff:3.500A) removed outlier: 5.318A 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: 3.538A pdb=" N SER24 17 " --> pdb=" O GLY24 13 " (cutoff:3.500A) Processing helix chain '24' and resid 43 through 52 removed outlier: 4.151A pdb=" N VAL24 47 " --> pdb=" O ASP24 43 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA24 52 " --> pdb=" O MET24 48 " (cutoff:3.500A) Processing helix chain '24' and resid 53 through 59 removed outlier: 4.103A pdb=" N TYR24 57 " --> pdb=" O LYS24 53 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER24 58 " --> pdb=" O ALA24 54 " (cutoff:3.500A) Processing helix chain '26' and resid 51 through 61 removed outlier: 3.516A pdb=" N MET26 55 " --> pdb=" O SER26 51 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG26 56 " --> pdb=" O ALA26 52 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL26 57 " --> pdb=" O LYS26 53 " (cutoff:3.500A) Processing helix chain '26' and resid 62 through 74 removed outlier: 3.570A pdb=" N ARG26 73 " --> pdb=" O GLU26 69 " (cutoff:3.500A) Processing helix chain '27' and resid 1 through 7 removed outlier: 3.867A pdb=" N LEU27 6 " --> pdb=" O LYS27 2 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ARG27 7 " --> pdb=" O ALA27 3 " (cutoff:3.500A) Processing helix chain '27' and resid 9 through 35 removed outlier: 3.590A pdb=" N GLU27 24 " --> pdb=" O ASN27 20 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN27 25 " --> pdb=" O LEU27 21 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE27 26 " --> pdb=" O LEU27 22 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG27 29 " --> pdb=" O GLN27 25 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN27 31 " --> pdb=" O ASN27 27 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA27 33 " --> pdb=" O ARG27 29 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER27 34 " --> pdb=" O MET27 30 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY27 35 " --> pdb=" O GLN27 31 " (cutoff:3.500A) Processing helix chain '27' and resid 40 through 62 removed outlier: 3.846A pdb=" N LYS27 44 " --> pdb=" O SER27 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA27 51 " --> pdb=" O ARG27 47 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY27 62 " --> pdb=" O ASN27 58 " (cutoff:3.500A) Processing helix chain '28' and resid 16 through 27 Processing helix chain '28' and resid 40 through 51 removed outlier: 4.097A pdb=" N MET28 46 " --> pdb=" O ALA28 42 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER28 51 " --> pdb=" O ILE28 47 " (cutoff:3.500A) Processing helix chain '29' and resid 43 through 53 removed outlier: 4.526A pdb=" N GLN29 48 " --> pdb=" O PHE29 44 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP29 50 " --> pdb=" O GLY29 46 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL29 51 " --> pdb=" O LYS29 47 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA29 52 " --> pdb=" O GLN29 48 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR29 53 " --> pdb=" O ARG29 49 " (cutoff:3.500A) Processing helix chain '29' and resid 55 through 65 removed outlier: 4.516A pdb=" N ARG29 59 " --> pdb=" O GLY29 55 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG29 63 " --> pdb=" O ARG29 59 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE29 64 " --> pdb=" O PHE29 60 " (cutoff:3.500A) Processing helix chain '30' and resid 8 through 20 removed outlier: 4.644A pdb=" N HIS30 18 " --> pdb=" O MET30 14 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP30 19 " --> pdb=" O ARG30 15 " (cutoff:3.500A) removed outlier: 3.878A 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: 4.494A pdb=" N THR32 24 " --> pdb=" O ALA32 20 " (cutoff:3.500A) Processing helix chain '32' and resid 25 through 38 Processing helix chain '33' and resid 6 through 14 removed outlier: 4.257A pdb=" N ARG33 12 " --> pdb=" O GLY33 8 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE33 13 " --> pdb=" O ALA33 9 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS33 14 " --> pdb=" O ALA33 10 " (cutoff:3.500A) Processing helix chain '33' and resid 31 through 36 removed outlier: 5.318A pdb=" N LYS33 35 " --> pdb=" O ILE33 31 " (cutoff:3.500A) removed outlier: 4.952A 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 removed outlier: 3.546A pdb=" N ARG33 44 " --> pdb=" O LYS33 40 " (cutoff:3.500A) Proline residue: 33 45 - end of helix Processing helix chain '33' and resid 51 through 62 removed outlier: 4.225A pdb=" N GLY33 55 " --> pdb=" O LYS33 51 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU33 56 " --> pdb=" O GLY33 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA33 59 " --> pdb=" O GLY33 55 " (cutoff:3.500A) Proline residue: 33 62 - end of helix Processing helix chain 'B' and resid 23 through 28 removed outlier: 4.060A pdb=" N LYS B 27 " --> pdb=" O ASN B 23 " (cutoff:3.500A) Proline residue: B 28 - end of helix No H-bonds generated for 'chain 'B' and resid 23 through 28' Processing helix chain 'B' and resid 41 through 63 Proline residue: B 47 - end of helix removed outlier: 3.529A pdb=" N SER B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 removed outlier: 3.834A pdb=" N SER B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 122 removed outlier: 3.544A pdb=" N VAL B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.666A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.936A pdb=" N GLU B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.677A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLY B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 225 removed outlier: 3.949A pdb=" N GLY B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.853A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.632A pdb=" N ASN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.878A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 4.185A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.211A 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: 3.888A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 removed outlier: 3.509A pdb=" N ARG C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 4.119A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.573A pdb=" N GLU D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.557A pdb=" N ASN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.588A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 removed outlier: 3.578A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 120 removed outlier: 4.106A pdb=" N LYS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 164 removed outlier: 3.700A pdb=" N ALA D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 3.543A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 191' Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.268A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 removed outlier: 3.658A pdb=" N ILE E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 5.660A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.567A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.678A 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: 5.566A 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 removed outlier: 4.159A pdb=" N LEU E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 removed outlier: 3.566A pdb=" N SER F 15 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLN F 17 " --> pdb=" O ASP F 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 11 through 17' Processing helix chain 'F' and resid 18 through 33 removed outlier: 3.684A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.789A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 76 " --> pdb=" O ASP F 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 removed outlier: 3.574A pdb=" N ALA G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 54 removed outlier: 3.638A pdb=" N SER G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 69 removed outlier: 3.738A pdb=" N ALA G 60 " --> pdb=" O SER G 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 removed outlier: 3.736A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLY G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 removed outlier: 3.668A pdb=" N ALA G 126 " --> pdb=" O GLU G 122 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 146 removed outlier: 3.646A pdb=" N LYS G 135 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 145 " --> pdb=" O HIS G 141 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 20 removed outlier: 3.558A pdb=" N ARG H 12 " --> pdb=" O ASP H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 43 removed outlier: 3.709A pdb=" N ALA H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'I' and resid 33 through 38 removed outlier: 3.792A pdb=" N PHE I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 55 removed outlier: 4.921A pdb=" N ARG I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Proline residue: I 50 - end of helix removed outlier: 4.606A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL I 54 " --> pdb=" O PRO I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 87 removed outlier: 3.522A pdb=" N THR I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 101 removed outlier: 4.097A pdb=" N ARG I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY I 101 " --> pdb=" O LEU I 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.703A pdb=" N ASP J 19 " --> pdb=" O HIS J 15 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 4.151A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 Processing helix chain 'K' and resid 53 through 59 removed outlier: 4.712A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 59 - end of helix No H-bonds generated for 'chain 'K' and resid 53 through 59' Processing helix chain 'K' and resid 60 through 73 removed outlier: 4.127A pdb=" N ASP K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 103 removed outlier: 5.297A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN K 100 " --> pdb=" O ILE K 96 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA K 101 " --> pdb=" O ARG K 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 9 Processing helix chain 'L' and resid 21 through 26 removed outlier: 6.048A pdb=" N ALA L 25 " --> pdb=" O PRO L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 117 removed outlier: 5.175A pdb=" N TYR L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 3.877A 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 22 removed outlier: 3.724A pdb=" N THR M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TYR M 22 " --> pdb=" O LEU M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 37 Processing helix chain 'M' and resid 43 through 48 removed outlier: 5.262A pdb=" N SER M 48 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 63 removed outlier: 3.647A pdb=" N ASP M 53 " --> pdb=" O GLU M 49 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU M 55 " --> pdb=" O GLN M 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL M 63 " --> pdb=" O VAL M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 removed outlier: 3.773A pdb=" N ARG M 70 " --> pdb=" O GLY M 66 " (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 20 removed outlier: 3.531A pdb=" N LYS N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA N 14 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE N 20 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 33 removed outlier: 5.489A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE N 29 " --> pdb=" O GLU N 25 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE N 30 " --> pdb=" O LEU N 26 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP N 32 " --> pdb=" O ALA N 28 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL N 33 " --> pdb=" O ILE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 50 removed outlier: 3.757A pdb=" N ALA N 43 " --> pdb=" O ASP N 39 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL N 44 " --> pdb=" O ARG N 40 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 3.728A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA N 87 " --> pdb=" O VAL N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 15 removed outlier: 3.767A pdb=" N LYS O 9 " --> pdb=" O GLU O 5 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER O 12 " --> pdb=" O ALA O 8 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU O 13 " --> pdb=" O LYS O 9 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY O 15 " --> pdb=" O VAL O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 43 removed outlier: 3.563A pdb=" N ILE O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 73 removed outlier: 3.970A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 84 removed outlier: 3.598A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG O 83 " --> pdb=" O GLN O 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.612A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 79 removed outlier: 3.708A pdb=" N VAL P 78 " --> pdb=" O LEU P 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 33 removed outlier: 4.395A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N THR R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.914A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 40 through 45' Processing helix chain 'R' and resid 47 through 65 removed outlier: 3.604A pdb=" N LYS R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 17 removed outlier: 5.519A pdb=" N VAL R 17 " --> pdb=" O PHE R 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 12 through 17' Processing helix chain 'S' and resid 11 through 25 removed outlier: 3.612A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 75 removed outlier: 4.825A pdb=" N PHE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA S 74 " --> pdb=" O LEU S 70 " (cutoff:3.500A) Proline residue: S 75 - end of helix No H-bonds generated for 'chain 'S' and resid 69 through 75' Processing helix chain 'T' and resid 6 through 41 removed outlier: 4.748A pdb=" N ALA T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA T 40 " --> pdb=" O ALA T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 64 Proline residue: T 55 - end of helix removed outlier: 3.548A pdb=" N ARG T 59 " --> pdb=" O PRO T 55 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY T 64 " --> pdb=" O GLN T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 86 removed outlier: 3.504A pdb=" N HIS T 74 " --> pdb=" O LYS T 70 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA T 80 " --> pdb=" O ALA T 76 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU T 85 " --> pdb=" O GLN T 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 22 removed outlier: 3.909A pdb=" N ARG U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER U 21 " --> pdb=" O ARG U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 34 removed outlier: 3.576A pdb=" N LEU U 28 " --> pdb=" O LYS U 24 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLU U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ARG U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 61 removed outlier: 3.688A pdb=" N THR U 42 " --> pdb=" O GLU U 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL U 52 " --> pdb=" O LYS U 48 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) Processing helix chain '03' and resid 6 through 16 removed outlier: 3.834A pdb=" N VAL03 10 " --> pdb=" O LYS03 6 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE03 11 " --> pdb=" O ARG03 7 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG03 12 " --> pdb=" O MET03 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS03 14 " --> pdb=" O VAL03 10 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL03 15 " --> pdb=" O ILE03 11 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP03 16 " --> pdb=" O ARG03 12 " (cutoff:3.500A) Processing helix chain '03' and resid 22 through 35 removed outlier: 3.561A pdb=" N ALA03 28 " --> pdb=" O ASN03 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU03 30 " --> pdb=" O ALA03 26 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS03 31 " --> pdb=" O ILE03 27 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU03 32 " --> pdb=" O ALA03 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU03 33 " --> pdb=" O LEU03 29 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA03 34 " --> pdb=" O LEU03 30 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR03 35 " --> pdb=" O LYS03 31 " (cutoff:3.500A) Processing helix chain '03' and resid 181 through 200 removed outlier: 4.105A pdb=" N GLU03 187 " --> pdb=" O ASP03 183 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN03 188 " --> pdb=" O LYS03 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU03 189 " --> pdb=" O LEU03 185 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU03 190 " --> pdb=" O LYS03 186 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU03 196 " --> pdb=" O LEU03 192 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS03 198 " --> pdb=" O VAL03 194 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA03 199 " --> pdb=" O ALA03 195 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 39 removed outlier: 3.871A pdb=" N LYS Z 37 " --> pdb=" O THR Z 33 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR Z 38 " --> pdb=" O VAL Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 51 removed outlier: 3.627A pdb=" N ASN Z 51 " --> pdb=" O ASP Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 59 removed outlier: 3.883A pdb=" N ALA Z 57 " --> pdb=" O PRO Z 53 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG Z 58 " --> pdb=" O GLU Z 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 99 removed outlier: 4.002A pdb=" N GLN Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET Z 98 " --> pdb=" O GLY Z 94 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP Z 99 " --> pdb=" O ALA Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 126 removed outlier: 3.541A pdb=" N VAL Z 125 " --> pdb=" O LEU Z 121 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY Z 126 " --> pdb=" O GLY Z 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 136 through 141 removed outlier: 4.168A pdb=" N VAL Z 140 " --> pdb=" O LYS Z 136 " (cutoff:3.500A) removed outlier: 4.998A 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: 3.873A pdb=" N LEU Z 146 " --> pdb=" O ASP Z 142 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU Z 148 " --> pdb=" O GLU Z 144 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP Z 161 " --> pdb=" O LEU Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 173 through 180 Processing helix chain 'Z' and resid 181 through 198 removed outlier: 3.734A pdb=" N LYS Z 187 " --> pdb=" O GLU Z 183 " (cutoff:3.500A) Processing helix chain 'Z' and resid 282 through 287 removed outlier: 3.844A pdb=" N ILE Z 286 " --> pdb=" O LYS Z 282 " (cutoff:3.500A) removed outlier: 5.136A 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 1 through 4 Processing sheet with id= 2, first strand: chain '04' and resid 72 through 78 removed outlier: 4.944A pdb=" N ILE04 73 " --> pdb=" O SER04 117 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER04 117 " --> pdb=" O ILE04 73 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP04 113 " --> pdb=" O VAL04 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '04' and resid 79 through 82 removed outlier: 3.739A pdb=" N ILE04 90 " --> pdb=" O GLU04 81 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASN04 89 " --> pdb=" O ALA04 105 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '04' and resid 127 through 130 removed outlier: 4.817A pdb=" N ASN04 127 " --> pdb=" O LEU04 191 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '04' and resid 137 through 140 removed outlier: 3.552A pdb=" N SER04 138 " --> pdb=" O ILE04 163 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR04 172 " --> pdb=" O VAL04 164 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU04 179 " --> pdb=" O LEU04 175 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '05' and resid 3 through 9 removed outlier: 4.287A pdb=" N SER05 199 " --> pdb=" O LYS05 8 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP05 200 " --> pdb=" O THR05 112 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR05 112 " --> pdb=" O ASP05 200 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '05' and resid 11 through 16 removed outlier: 3.689A pdb=" N ILE05 22 " --> pdb=" O ILE05 14 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL05 20 " --> pdb=" O THR05 16 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '05' and resid 36 through 40 removed outlier: 6.400A pdb=" N GLN05 36 " --> pdb=" O ILE05 48 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE05 48 " --> pdb=" O GLN05 36 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS05 38 " --> pdb=" O ARG05 46 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG05 46 " --> pdb=" O LYS05 38 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU05 40 " --> pdb=" O GLY05 44 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN05 49 " --> pdb=" O THR05 35 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN05 94 " --> pdb=" O VAL05 34 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '05' and resid 46 through 51 removed outlier: 5.739A pdb=" N ARG05 46 " --> pdb=" O LEU05 84 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '06' and resid 1 through 5 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain '06' and resid 117 through 120 removed outlier: 3.995A pdb=" N ASP06 168 " --> pdb=" O VAL06 146 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '07' and resid 64 through 68 removed outlier: 3.599A pdb=" N LYS07 32 " --> pdb=" O THR07 156 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN07 36 " --> pdb=" O ASP07 152 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLY07 38 " --> pdb=" O GLY07 150 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY07 150 " --> pdb=" O GLY07 38 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU07 151 " --> pdb=" O VAL07 131 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '08' and resid 14 through 19 removed outlier: 7.035A pdb=" N GLN08 21 " --> pdb=" O LEU08 36 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU08 36 " --> pdb=" O GLN08 21 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE08 23 " --> pdb=" O ARG08 34 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG08 34 " --> pdb=" O ILE08 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY08 30 " --> pdb=" O GLY08 27 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '08' and resid 39 through 44 removed outlier: 7.650A pdb=" N ALA08 39 " --> pdb=" O ARG08 54 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '08' and resid 81 through 88 removed outlier: 3.522A pdb=" N GLY08 134 " --> pdb=" O PHE08 82 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR08 128 " --> pdb=" O LEU08 88 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '08' and resid 100 through 105 removed outlier: 6.685A pdb=" N ASN08 100 " --> pdb=" O LEU08 116 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '09' and resid 76 through 83 removed outlier: 8.005A pdb=" N GLU09 76 " --> pdb=" O LYS09 141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU09 149 " --> pdb=" O SER09 82 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '10' and resid 24 through 28 removed outlier: 4.418A pdb=" N ALA10 25 " --> pdb=" O SER10 85 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '11' and resid 7 through 10 removed outlier: 4.027A pdb=" N VAL11 57 " --> pdb=" O VAL11 69 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL11 69 " --> pdb=" O VAL11 57 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '11' and resid 98 through 101 Processing sheet with id= 21, first strand: chain '12' and resid 52 through 57 removed outlier: 5.443A pdb=" N ASP12 19 " --> pdb=" O LEU12 140 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '12' and resid 74 through 78 removed outlier: 7.340A pdb=" N GLY12 83 " --> pdb=" O THR12 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '13' and resid 18 through 21 removed outlier: 3.646A pdb=" N THR13 6 " --> pdb=" O CYS13 21 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN13 82 " --> pdb=" O MET13 7 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '15' and resid 37 through 40 removed outlier: 3.549A pdb=" N LYS15 71 " --> pdb=" O VAL15 93 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '15' and resid 62 through 66 removed outlier: 6.236A 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: 3.605A pdb=" N MET15 105 " --> pdb=" O PHE15 31 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER15 30 " --> pdb=" O LYS15 133 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS15 133 " --> pdb=" O SER15 30 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS15 127 " --> pdb=" O VAL15 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '16' and resid 33 through 36 removed outlier: 5.927A pdb=" N MET16 110 " --> pdb=" O CYS16 100 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR16 112 " --> pdb=" O LEU16 98 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU16 114 " --> pdb=" O ARG16 96 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR16 94 " --> pdb=" O VAL16 116 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '17' and resid 49 through 53 removed outlier: 3.886A pdb=" N VAL17 49 " --> pdb=" O VAL17 39 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE17 35 " --> pdb=" O THR17 53 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG17 25 " --> pdb=" O ILE17 40 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL17 28 " --> pdb=" O ASP17 93 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '18' and resid 37 through 44 Processing sheet with id= 29, first strand: chain '18' and resid 48 through 51 removed outlier: 3.641A pdb=" N ALA18 48 " --> pdb=" O THR18 59 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N SER18 56 " --> pdb=" O THR18 75 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '20' and resid 11 through 15 removed outlier: 3.609A pdb=" N VAL20 4 " --> pdb=" O MET20 40 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET20 40 " --> pdb=" O VAL20 4 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '20' and resid 17 through 22 removed outlier: 6.465A pdb=" N ASP20 95 " --> pdb=" O VAL20 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS20 60 " --> pdb=" O THR20 99 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '20' and resid 57 through 60 removed outlier: 4.332A pdb=" N VAL20 58 " --> pdb=" O SER20 102 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '20' and resid 65 through 68 removed outlier: 3.774A pdb=" N ALA20 65 " --> pdb=" O ASP20 95 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY20 67 " --> pdb=" O PHE20 93 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '20' and resid 69 through 78 removed outlier: 5.297A pdb=" N GLU20 70 " --> pdb=" O GLN20 91 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN20 91 " --> pdb=" O GLU20 70 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR20 83 " --> pdb=" O ARG20 78 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '21' and resid 2 through 8 removed outlier: 4.720A pdb=" N THR21 3 " --> pdb=" O VAL21 107 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL21 107 " --> pdb=" O THR21 3 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '22' and resid 28 through 34 removed outlier: 6.313A pdb=" N ASN22 28 " --> pdb=" O LEU22 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE22 30 " --> pdb=" O VAL22 85 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS22 81 " --> pdb=" O VAL22 34 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS22 66 " --> pdb=" O ARG22 77 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP22 79 " --> pdb=" O LYS22 64 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS22 64 " --> pdb=" O ASP22 79 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS22 81 " --> pdb=" O VAL22 62 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL22 62 " --> pdb=" O LYS22 81 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA22 83 " --> pdb=" O THR22 60 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR22 60 " --> pdb=" O ALA22 83 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL22 85 " --> pdb=" O VAL22 58 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL22 58 " --> pdb=" O VAL22 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '23' and resid 39 through 44 removed outlier: 4.950A pdb=" N ASN23 39 " --> pdb=" O ALA23 62 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '23' and resid 82 through 86 Processing sheet with id= 39, first strand: chain '24' and resid 2 through 5 Processing sheet with id= 40, first strand: chain '24' and resid 37 through 42 removed outlier: 3.789A pdb=" N ILE24 89 " --> pdb=" O PRO24 27 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '25' and resid 46 through 50 removed outlier: 8.376A pdb=" N ASN25 46 " --> pdb=" O LYS25 58 " (cutoff:3.500A) removed outlier: 4.148A 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 removed outlier: 3.593A pdb=" N LYS25 62 " --> pdb=" O GLU25 79 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '26' and resid 11 through 18 removed outlier: 3.536A pdb=" N VAL26 12 " --> pdb=" O PHE26 28 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER26 18 " --> pdb=" O ASN26 22 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN26 22 " --> pdb=" O SER26 18 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '26' and resid 34 through 40 Processing sheet with id= 45, first strand: chain '28' and resid 34 through 38 removed outlier: 4.136A pdb=" N LYS28 5 " --> pdb=" O GLU28 57 " (cutoff:3.500A) removed outlier: 7.250A 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 '31' and resid 18 through 23 removed outlier: 6.473A pdb=" N HIS31 18 " --> pdb=" O SER31 12 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE31 47 " --> pdb=" O SER31 13 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU31 33 " --> pdb=" O GLU31 50 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '34' and resid 13 through 19 removed outlier: 8.392A pdb=" N ASN34 13 " --> pdb=" O SER34 28 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER34 28 " --> pdb=" O ASN34 13 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE34 26 " --> pdb=" O LYS34 15 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N CYS34 27 " --> pdb=" O HIS34 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS34 33 " --> pdb=" O CYS34 27 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.320A pdb=" N VAL B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'B' and resid 88 through 91 removed outlier: 3.533A pdb=" N ILE B 185 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 197 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 184 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 18 through 21 removed outlier: 6.044A pdb=" N ASN C 18 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 58 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 65 " --> pdb=" O GLN C 99 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 163 through 170 removed outlier: 3.508A pdb=" N GLY C 154 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 201 " --> pdb=" O ASP C 182 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP C 180 " --> pdb=" O LYS C 203 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU C 205 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG C 178 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'D' and resid 140 through 143 removed outlier: 6.066A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'E' and resid 10 through 15 removed outlier: 6.551A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'E' and resid 82 through 87 removed outlier: 7.278A pdb=" N HIS E 82 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 93 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG E 92 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR E 127 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 123 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'E' and resid 31 through 40 removed outlier: 4.618A pdb=" N GLY E 50 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.776A pdb=" N LEU F 61 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP F 42 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE F 6 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR F 92 " --> pdb=" O HIS F 3 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU F 5 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'G' and resid 72 through 76 Processing sheet with id= 59, first strand: chain 'H' and resid 22 through 28 removed outlier: 5.956A pdb=" N ALA H 22 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU H 51 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR H 61 " --> pdb=" O ASP H 47 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'H' and resid 73 through 76 removed outlier: 4.417A pdb=" N SER H 73 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'I' and resid 4 through 10 removed outlier: 3.512A pdb=" N TYR I 5 " --> pdb=" O ILE I 20 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY I 9 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS I 67 " --> pdb=" O ALA I 15 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE I 19 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS I 26 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'J' and resid 35 through 38 removed outlier: 8.243A pdb=" N GLN J 35 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA J 12 " --> pdb=" O HIS J 70 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE J 8 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.878A pdb=" N LEU J 42 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'J' and resid 44 through 52 removed outlier: 6.623A pdb=" N GLU J 47 " --> pdb=" O ILE J 67 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'K' and resid 30 through 34 removed outlier: 6.360A pdb=" N ILE K 109 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL K 83 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASP K 111 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL K 85 " --> pdb=" O ASP K 111 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'L' and resid 28 through 31 removed outlier: 5.175A pdb=" N LEU L 80 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'L' and resid 35 through 40 removed outlier: 4.507A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS L 52 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.687A pdb=" N ALA P 7 " --> pdb=" O GLN P 18 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLN P 18 " --> pdb=" O ALA P 7 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'P' and resid 37 through 40 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 'Q' and resid 6 through 10 removed outlier: 3.520A pdb=" N GLY Q 9 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.989A 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 30 removed outlier: 4.896A pdb=" N LYS Q 18 " --> pdb=" O ASP Q 47 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS Q 35 " --> pdb=" O HIS Q 30 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'S' and resid 47 through 51 removed outlier: 3.707A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL S 59 " --> pdb=" O ILE S 48 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '03' and resid 60 through 64 removed outlier: 4.050A pdb=" N GLY03 61 " --> pdb=" O TYR03 163 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain '03' and resid 169 through 177 removed outlier: 5.655A pdb=" N GLY03 169 " --> pdb=" O LEU03 48 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL03 46 " --> pdb=" O ILE03 171 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR03 173 " --> pdb=" O VAL03 44 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL03 44 " --> pdb=" O THR03 173 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS03 177 " --> pdb=" O GLU03 40 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU03 40 " --> pdb=" O LYS03 177 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS03 211 " --> pdb=" O ASN03 47 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL03 212 " --> pdb=" O VAL03 224 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Z' and resid 64 through 71 removed outlier: 3.698A pdb=" N TYR Z 69 " --> pdb=" O TYR Z 76 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY Z 100 " --> pdb=" O ASN Z 13 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY Z 15 " --> pdb=" O GLY Z 100 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL Z 132 " --> pdb=" O PRO Z 168 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL Z 170 " --> pdb=" O VAL Z 132 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Z' and resid 210 through 215 removed outlier: 7.193A pdb=" N PHE Z 210 " --> pdb=" O LYS Z 294 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS Z 294 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU Z 212 " --> pdb=" O LEU Z 292 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN Z 290 " --> pdb=" O ILE Z 214 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA Z 293 " --> pdb=" O GLU Z 243 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Z' and resid 216 through 219 Processing sheet with id= 78, first strand: chain 'Z' and resid 328 through 332 removed outlier: 3.552A pdb=" N GLN Z 329 " --> pdb=" O ARG Z 377 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU Z 372 " --> pdb=" O VAL Z 388 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE Z 376 " --> pdb=" O GLY Z 384 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'Z' and resid 303 through 306 removed outlier: 4.220A pdb=" N LYS Z 303 " --> pdb=" O LEU Z 392 " (cutoff:3.500A) 1737 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3464 hydrogen bonds 5700 hydrogen bond angles 0 basepair planarities 1394 basepair parallelities 2878 stacking parallelities Total time for adding SS restraints: 299.95 Time building geometry restraints manager: 60.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 30536 1.34 - 1.47: 70995 1.47 - 1.59: 56374 1.59 - 1.72: 8608 1.72 - 1.85: 309 Bond restraints: 166822 Sorted by residual: bond pdb=" O3A GCP Z 402 " pdb=" PB GCP Z 402 " ideal model delta sigma weight residual 1.697 1.522 0.175 2.00e-02 2.50e+03 7.64e+01 bond pdb=" C5 U8U Y 34 " pdb=" C6 U8U Y 34 " ideal model delta sigma weight residual 1.491 1.360 0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" N1 U8U Y 34 " pdb=" C2 U8U Y 34 " ideal model delta sigma weight residual 1.492 1.389 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C2 U8U Y 34 " pdb=" S2 U8U Y 34 " ideal model delta sigma weight residual 1.598 1.698 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O3A GCP Z 402 " pdb=" PA GCP Z 402 " ideal model delta sigma weight residual 1.621 1.528 0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 166817 not shown) Histogram of bond angle deviations from ideal: 93.27 - 104.98: 22291 104.98 - 116.69: 127123 116.69 - 128.40: 91967 128.40 - 140.11: 7694 140.11 - 151.82: 2 Bond angle restraints: 249077 Sorted by residual: angle pdb=" O3' A A 246 " pdb=" C3' A A 246 " pdb=" C2' A A 246 " ideal model delta sigma weight residual 109.50 127.11 -17.61 1.50e+00 4.44e-01 1.38e+02 angle pdb=" N LEU14 95 " pdb=" CA LEU14 95 " pdb=" C LEU14 95 " ideal model delta sigma weight residual 112.89 98.71 14.18 1.24e+00 6.50e-01 1.31e+02 angle pdb=" N VAL10 77 " pdb=" CA VAL10 77 " pdb=" C VAL10 77 " ideal model delta sigma weight residual 111.91 102.40 9.51 8.90e-01 1.26e+00 1.14e+02 angle pdb=" N MET Z 98 " pdb=" CA MET Z 98 " pdb=" C MET Z 98 " ideal model delta sigma weight residual 110.43 124.02 -13.59 1.31e+00 5.83e-01 1.08e+02 angle pdb=" N ARG04 12 " pdb=" CA ARG04 12 " pdb=" C ARG04 12 " ideal model delta sigma weight residual 112.88 100.03 12.85 1.29e+00 6.01e-01 9.92e+01 ... (remaining 249072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 86339 35.73 - 71.45: 2812 71.45 - 107.18: 247 107.18 - 142.90: 14 142.90 - 178.63: 19 Dihedral angle restraints: 89431 sinusoidal: 70999 harmonic: 18432 Sorted by residual: dihedral pdb=" C5' A A 246 " pdb=" C4' A A 246 " pdb=" C3' A A 246 " pdb=" O3' A A 246 " ideal model delta sinusoidal sigma weight residual 147.00 80.14 66.86 1 8.00e+00 1.56e-02 9.11e+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 29.35 170.65 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U011915 " pdb=" C1' U011915 " pdb=" N1 U011915 " pdb=" C2 U011915 " ideal model delta sinusoidal sigma weight residual 200.00 33.46 166.54 1 1.50e+01 4.44e-03 8.42e+01 ... (remaining 89428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.396: 31768 0.396 - 0.793: 13 0.793 - 1.189: 0 1.189 - 1.585: 0 1.585 - 1.982: 1 Chirality restraints: 31782 Sorted by residual: chirality pdb=" C3' A A 246 " pdb=" C4' A A 246 " pdb=" O3' A A 246 " pdb=" C2' A A 246 " both_signs ideal model delta sigma weight residual False -2.74 -0.76 -1.98 2.00e-01 2.50e+01 9.82e+01 chirality pdb=" P G Y 1 " pdb=" OP1 G Y 1 " pdb=" OP2 G Y 1 " pdb=" O5' G Y 1 " both_signs ideal model delta sigma weight residual True 2.41 3.06 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C3' GCP Z 402 " pdb=" C2' GCP Z 402 " pdb=" C4' GCP Z 402 " pdb=" O3' GCP Z 402 " both_signs ideal model delta sigma weight residual False -2.57 -3.21 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 31779 not shown) Planarity restraints: 13715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N FME W 101 " -0.225 2.00e-02 2.50e+03 1.84e-01 3.38e+02 pdb=" CA FME W 101 " 0.088 2.00e-02 2.50e+03 pdb=" CN FME W 101 " 0.252 2.00e-02 2.50e+03 pdb=" O1 FME W 101 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C X 69 " -0.111 2.00e-02 2.50e+03 5.54e-02 6.90e+01 pdb=" N1 C X 69 " 0.012 2.00e-02 2.50e+03 pdb=" C2 C X 69 " 0.020 2.00e-02 2.50e+03 pdb=" O2 C X 69 " 0.049 2.00e-02 2.50e+03 pdb=" N3 C X 69 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C X 69 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C X 69 " -0.077 2.00e-02 2.50e+03 pdb=" C5 C X 69 " 0.048 2.00e-02 2.50e+03 pdb=" C6 C X 69 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U01 562 " -0.095 2.00e-02 2.50e+03 5.32e-02 6.36e+01 pdb=" N1 U01 562 " 0.003 2.00e-02 2.50e+03 pdb=" C2 U01 562 " 0.019 2.00e-02 2.50e+03 pdb=" O2 U01 562 " 0.035 2.00e-02 2.50e+03 pdb=" N3 U01 562 " 0.020 2.00e-02 2.50e+03 pdb=" C4 U01 562 " 0.020 2.00e-02 2.50e+03 pdb=" O4 U01 562 " -0.097 2.00e-02 2.50e+03 pdb=" C5 U01 562 " 0.052 2.00e-02 2.50e+03 pdb=" C6 U01 562 " 0.043 2.00e-02 2.50e+03 ... (remaining 13712 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 1 2.03 - 2.75: 16027 2.75 - 3.47: 204690 3.47 - 4.18: 501348 4.18 - 4.90: 670873 Nonbonded interactions: 1392939 Sorted by model distance: nonbonded pdb=" O3' A Y 76 " pdb=" C LYS Y 101 " model vdw 1.314 3.270 nonbonded pdb=" O2' A Y 69 " pdb=" O5' C Y 70 " model vdw 2.250 2.440 nonbonded pdb=" O3' A Y 76 " pdb=" O LYS Y 101 " model vdw 2.253 3.040 nonbonded pdb=" O2' A Y 76 " pdb=" O LYS Y 101 " model vdw 2.253 2.440 nonbonded pdb=" O2' A Y 69 " pdb=" O4' C Y 70 " model vdw 2.328 2.440 ... (remaining 1392934 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: 6 Type Number sf(0) Gaussians P 4807 5.49 5 Mg 1 5.21 5 S 173 5.16 5 C 77705 2.51 5 N 28576 2.21 5 O 42497 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: 4.170 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: 0.090 Extract box with map and model: 31.610 Check model and map are aligned: 1.630 Convert atoms to be neutral: 0.980 Process input model: 591.710 Find NCS groups from input model: 3.380 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: 0.020 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 636.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 0.175 166822 Z= 0.419 Angle : 1.047 27.051 249077 Z= 0.692 Chirality : 0.089 1.982 31782 Planarity : 0.009 0.184 13715 Dihedral : 14.220 178.629 77545 Min Nonbonded Distance : 1.314 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 2.72 % Allowed : 13.87 % Favored : 83.41 % Rotamer Outliers : 1.29 % 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: -5.24 (0.08), residues: 6366 helix: -3.68 (0.07), residues: 1829 sheet: -3.11 (0.14), residues: 1049 loop : -3.57 (0.08), residues: 3488 *********************** 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 1882 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1814 time to evaluate : 6.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 9 residues processed: 1865 average time/residue: 1.5370 time to fit residues: 4902.5006 Evaluate side-chains 1033 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1024 time to evaluate : 6.794 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 1.6630 time to fit residues: 31.7014 ------------------------------------------------------------------------------- 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: 2.9990 chunk 285 optimal weight: 20.0000 chunk 562 optimal weight: 1.9990 chunk 445 optimal weight: 20.0000 chunk 862 optimal weight: 20.0000 chunk 333 optimal weight: 30.0000 chunk 524 optimal weight: 6.9990 chunk 642 optimal weight: 20.0000 chunk 999 optimal weight: 20.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- 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 04 133 ASN ** 04 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 238 ASN 05 32 ASN ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 173 GLN ** 06 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 06 97 ASN 06 163 ASN 06 195 GLN 07 62 GLN 08 19 ASN 08 44 HIS 08 47 ASN 08 110 HIS 09 43 ASN 09 128 HIS 10 88 HIS 10 122 GLN 11 18 ASN ** 11 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 93 ASN 11 106 GLN ** 12 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 90 ASN 16 18 GLN ** 16 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 19 GLN 17 29 HIS 18 55 HIS 18 65 ASN 18 114 ASN 19 36 GLN ** 19 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 80 ASN ** 20 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 18 GLN 20 82 HIS 21 57 ASN 22 59 ASN 22 72 GLN 23 53 GLN 23 68 ASN 23 73 ASN ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 25 72 ASN 26 15 ASN 27 20 ASN 28 19 HIS ** 28 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 61 ASN 33 27 ASN 33 42 HIS 34 35 GLN B 23 ASN B 35 ASN B 41 ASN B 121 GLN B 189 ASN C 2 GLN C 18 ASN C 24 ASN D 70 GLN D 115 GLN D 125 ASN D 135 GLN D 151 GLN D 195 ASN E 134 ASN E 145 ASN F 11 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS F 58 HIS F 63 ASN F 68 GLN G 27 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 HIS H 3 GLN ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 GLN I 31 GLN I 36 GLN I 74 GLN K 21 HIS K 37 GLN K 63 GLN L 4 ASN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 34 ASN N 61 ASN O 61 GLN R 51 GLN ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 HIS T 54 GLN 03 168 ASN 03 188 ASN ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 329 GLN Total number of N/Q/H flips: 88 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.114 166822 Z= 0.334 Angle : 0.809 14.649 249077 Z= 0.418 Chirality : 0.044 0.318 31782 Planarity : 0.007 0.107 13715 Dihedral : 14.300 178.659 64882 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.05 % Favored : 87.50 % Rotamer Outliers : 4.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.09), residues: 6366 helix: -1.96 (0.10), residues: 1932 sheet: -2.59 (0.14), residues: 1137 loop : -3.09 (0.09), residues: 3297 *********************** 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 1370 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1122 time to evaluate : 6.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 248 outliers final: 144 residues processed: 1264 average time/residue: 1.5237 time to fit residues: 3370.6131 Evaluate side-chains 1040 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 896 time to evaluate : 6.869 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 144 outliers final: 1 residues processed: 144 average time/residue: 1.2758 time to fit residues: 355.2748 ------------------------------------------------------------------------------- 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: 9.9990 chunk 310 optimal weight: 5.9990 chunk 832 optimal weight: 20.0000 chunk 680 optimal weight: 20.0000 chunk 275 optimal weight: 0.2980 chunk 1001 optimal weight: 20.0000 chunk 1082 optimal weight: 1.9990 chunk 892 optimal weight: 30.0000 chunk 993 optimal weight: 20.0000 chunk 341 optimal weight: 9.9990 chunk 803 optimal weight: 20.0000 overall best weight: 5.6588 ------------------------------------------------------------------------------- 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 04 162 GLN ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 110 GLN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 15 13 HIS ** 16 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 36 GLN 20 6 GLN ** 20 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 45 GLN ** 24 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 36 GLN ** 28 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 27 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN C 99 GLN C 122 GLN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN E 69 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 GLN K 39 ASN K 63 GLN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 HIS ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 HIS R 30 ASN ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 51 HIS S 55 GLN S 56 HIS ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 273 ASN ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 319 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.159 166822 Z= 0.207 Angle : 0.657 20.644 249077 Z= 0.340 Chirality : 0.037 0.298 31782 Planarity : 0.005 0.110 13715 Dihedral : 14.425 178.828 64882 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.51 % Favored : 88.14 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.10), residues: 6366 helix: -1.25 (0.11), residues: 1948 sheet: -2.43 (0.14), residues: 1162 loop : -2.71 (0.10), residues: 3256 *********************** 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 1213 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1065 time to evaluate : 6.826 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 outliers start: 148 outliers final: 65 residues processed: 1172 average time/residue: 1.4358 time to fit residues: 2948.1792 Evaluate side-chains 950 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 885 time to evaluate : 6.880 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 1.2371 time to fit residues: 159.1112 ------------------------------------------------------------------------------- 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: 30.0000 chunk 519 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 478 optimal weight: 0.0470 chunk 672 optimal weight: 30.0000 chunk 1005 optimal weight: 20.0000 chunk 1064 optimal weight: 5.9990 chunk 525 optimal weight: 7.9990 chunk 952 optimal weight: 40.0000 chunk 286 optimal weight: 20.0000 overall best weight: 8.4088 ------------------------------------------------------------------------------- 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 ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 08 29 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 30 GLN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 93 GLN 16 18 GLN 17 19 GLN 17 116 GLN ** 18 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 20 ASN 33 27 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS K 63 GLN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 HIS ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS M 104 ASN P 26 ASN ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 03 160 GLN ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.114 166822 Z= 0.273 Angle : 0.694 15.501 249077 Z= 0.357 Chirality : 0.038 0.301 31782 Planarity : 0.006 0.089 13715 Dihedral : 14.757 179.430 64882 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.97 % Favored : 87.70 % Rotamer Outliers : 3.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.10), residues: 6366 helix: -1.05 (0.11), residues: 1936 sheet: -2.30 (0.14), residues: 1143 loop : -2.62 (0.10), residues: 3287 *********************** 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 1144 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 948 time to evaluate : 6.801 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 outliers start: 196 outliers final: 114 residues processed: 1060 average time/residue: 1.3972 time to fit residues: 2605.3847 Evaluate side-chains 960 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 846 time to evaluate : 6.906 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 0 residues processed: 114 average time/residue: 1.1835 time to fit residues: 264.8876 ------------------------------------------------------------------------------- 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: 6.9990 chunk 15 optimal weight: 30.0000 chunk 792 optimal weight: 20.0000 chunk 439 optimal weight: 9.9990 chunk 908 optimal weight: 20.0000 chunk 735 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 543 optimal weight: 9.9990 chunk 955 optimal weight: 50.0000 chunk 268 optimal weight: 40.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- 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** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 04 250 GLN 05 130 GLN 05 134 HIS ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 08 19 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 11 ASN ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN 13 93 GLN 15 3 GLN ** 15 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 88 ASN ** 18 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 03 160 GLN ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 HIS ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.146 166822 Z= 0.346 Angle : 0.754 15.262 249077 Z= 0.386 Chirality : 0.041 0.312 31782 Planarity : 0.006 0.101 13715 Dihedral : 15.305 178.933 64882 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 29.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.34 % Favored : 86.35 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.10), residues: 6366 helix: -1.09 (0.11), residues: 1928 sheet: -2.39 (0.14), residues: 1162 loop : -2.57 (0.10), residues: 3276 *********************** 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 1054 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 884 time to evaluate : 6.699 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 outliers start: 170 outliers final: 100 residues processed: 999 average time/residue: 1.4042 time to fit residues: 2480.9734 Evaluate side-chains 916 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 816 time to evaluate : 6.821 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 0 residues processed: 100 average time/residue: 1.1749 time to fit residues: 230.5824 ------------------------------------------------------------------------------- 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: 9.9990 chunk 958 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 624 optimal weight: 30.0000 chunk 262 optimal weight: 2.9990 chunk 1065 optimal weight: 9.9990 chunk 884 optimal weight: 30.0000 chunk 493 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 chunk 352 optimal weight: 6.9990 chunk 559 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 05 134 HIS ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 5 GLN ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 110 GLN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 15 22 GLN ** 15 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 9 GLN ** 18 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 48 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN K 80 ASN L 4 ASN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.160 166822 Z= 0.250 Angle : 0.674 16.102 249077 Z= 0.346 Chirality : 0.037 0.323 31782 Planarity : 0.005 0.095 13715 Dihedral : 15.244 178.493 64882 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.08 % Favored : 87.65 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.10), residues: 6366 helix: -0.89 (0.11), residues: 1956 sheet: -2.27 (0.14), residues: 1139 loop : -2.46 (0.10), residues: 3271 *********************** 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 1041 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 901 time to evaluate : 8.996 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 outliers start: 140 outliers final: 76 residues processed: 975 average time/residue: 1.4501 time to fit residues: 2513.8271 Evaluate side-chains 900 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 824 time to evaluate : 6.255 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 1.2187 time to fit residues: 182.3901 ------------------------------------------------------------------------------- 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: 30.0000 chunk 606 optimal weight: 40.0000 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: 40.0000 chunk 664 optimal weight: 20.0000 chunk 646 optimal weight: 30.0000 chunk 489 optimal weight: 30.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- 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** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 110 HIS ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 16 18 GLN ** 18 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 15 GLN ** 23 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN F 37 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.174 166822 Z= 0.719 Angle : 1.176 18.253 249077 Z= 0.581 Chirality : 0.057 0.385 31782 Planarity : 0.009 0.134 13715 Dihedral : 17.078 178.137 64882 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 51.36 Ramachandran Plot: Outliers : 0.41 % Allowed : 17.04 % Favored : 82.55 % Rotamer Outliers : 3.84 % 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: -3.86 (0.09), residues: 6366 helix: -1.93 (0.10), residues: 1909 sheet: -2.57 (0.14), residues: 1070 loop : -2.98 (0.10), residues: 3387 *********************** 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: 203 poor density : 784 time to evaluate : 6.667 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 outliers start: 203 outliers final: 132 residues processed: 912 average time/residue: 1.3570 time to fit residues: 2185.9855 Evaluate side-chains 853 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 721 time to evaluate : 6.562 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 0 residues processed: 132 average time/residue: 1.1500 time to fit residues: 293.8765 ------------------------------------------------------------------------------- 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: 10.0000 chunk 423 optimal weight: 10.0000 chunk 633 optimal weight: 20.0000 chunk 319 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 674 optimal weight: 10.0000 chunk 722 optimal weight: 7.9990 chunk 524 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 834 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 05 134 HIS ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 6 GLN ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 62 ASN ** 18 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 25 53 HIS ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 33 HIS 28 48 ASN 29 48 GLN 31 18 HIS ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN G 85 GLN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 ASN O 79 GLN ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.176 166822 Z= 0.227 Angle : 0.713 16.817 249077 Z= 0.365 Chirality : 0.039 0.333 31782 Planarity : 0.006 0.128 13715 Dihedral : 16.085 179.252 64882 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 25.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.83 % Favored : 87.89 % Rotamer Outliers : 1.72 % 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: -3.15 (0.10), residues: 6366 helix: -1.15 (0.11), residues: 1933 sheet: -2.32 (0.14), residues: 1099 loop : -2.62 (0.10), residues: 3334 *********************** 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 984 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 893 time to evaluate : 6.678 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: 91 outliers final: 46 residues processed: 948 average time/residue: 1.4900 time to fit residues: 2513.5895 Evaluate side-chains 840 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 794 time to evaluate : 6.888 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 1.2895 time to fit residues: 117.5387 ------------------------------------------------------------------------------- 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: 20.0000 chunk 1016 optimal weight: 30.0000 chunk 927 optimal weight: 20.0000 chunk 988 optimal weight: 20.0000 chunk 595 optimal weight: 30.0000 chunk 430 optimal weight: 20.0000 chunk 776 optimal weight: 20.0000 chunk 303 optimal weight: 20.0000 chunk 893 optimal weight: 20.0000 chunk 935 optimal weight: 20.0000 chunk 985 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- 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** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 04 250 GLN ** 05 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 134 HIS ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 16 18 GLN ** 18 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 51 GLN 21 7 HIS ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 48 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.186 166822 Z= 0.559 Angle : 0.984 16.847 249077 Z= 0.493 Chirality : 0.050 0.482 31782 Planarity : 0.008 0.133 13715 Dihedral : 16.812 179.827 64882 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 43.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 16.53 % Favored : 83.19 % Rotamer Outliers : 2.31 % 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: -3.66 (0.09), residues: 6366 helix: -1.65 (0.11), residues: 1912 sheet: -2.53 (0.14), residues: 1078 loop : -2.91 (0.10), residues: 3376 *********************** 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 892 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 770 time to evaluate : 6.914 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 outliers start: 122 outliers final: 81 residues processed: 836 average time/residue: 1.3513 time to fit residues: 1998.6489 Evaluate side-chains 826 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 745 time to evaluate : 6.801 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 1.1803 time to fit residues: 186.1467 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1045 optimal weight: 40.0000 chunk 638 optimal weight: 20.0000 chunk 496 optimal weight: 8.9990 chunk 726 optimal weight: 10.0000 chunk 1096 optimal weight: 0.6980 chunk 1009 optimal weight: 10.0000 chunk 873 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 674 optimal weight: 20.0000 chunk 535 optimal weight: 20.0000 overall best weight: 7.3392 ------------------------------------------------------------------------------- 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** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 04 250 GLN ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 42 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 16 18 GLN ** 18 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 19 19 GLN ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 48 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** 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: 0.8057 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.285 166822 Z= 0.250 Angle : 0.731 18.691 249077 Z= 0.375 Chirality : 0.039 0.310 31782 Planarity : 0.006 0.134 13715 Dihedral : 16.266 179.806 64882 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 28.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.60 % Favored : 87.21 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.10), residues: 6366 helix: -1.23 (0.11), residues: 1919 sheet: -2.32 (0.14), residues: 1103 loop : -2.67 (0.10), residues: 3344 ********************** 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 886 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 841 time to evaluate : 6.569 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 outliers start: 45 outliers final: 28 residues processed: 862 average time/residue: 1.3457 time to fit residues: 2055.4848 Evaluate side-chains 826 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 798 time to evaluate : 6.878 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 1.2036 time to fit residues: 70.5942 ------------------------------------------------------------------------------- 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: 30.0000 chunk 267 optimal weight: 6.9990 chunk 805 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 242 optimal weight: 20.0000 chunk 874 optimal weight: 20.0000 chunk 366 optimal weight: 5.9990 chunk 898 optimal weight: 30.0000 chunk 110 optimal weight: 40.0000 chunk 161 optimal weight: 10.0000 overall best weight: 12.5996 ------------------------------------------------------------------------------- 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** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 04 250 GLN ** 05 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 15 3 GLN 16 18 GLN ** 18 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 GLN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.042714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.036986 restraints weight = 1526712.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.037927 restraints weight = 613163.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.038473 restraints weight = 329415.435| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.190 166822 Z= 0.372 Angle : 0.803 19.257 249077 Z= 0.408 Chirality : 0.042 0.297 31782 Planarity : 0.006 0.122 13715 Dihedral : 16.423 179.371 64882 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 34.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.22 % Favored : 84.56 % Rotamer Outliers : 0.87 % 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: -3.26 (0.10), residues: 6366 helix: -1.28 (0.11), residues: 1921 sheet: -2.32 (0.15), residues: 1067 loop : -2.69 (0.10), residues: 3378 =============================================================================== Job complete usr+sys time: 39096.35 seconds wall clock time: 677 minutes 58.75 seconds (40678.75 seconds total)