Starting phenix.real_space_refine on Sun Feb 18 19:19:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/02_2024/7qtt_14146_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/02_2024/7qtt_14146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/02_2024/7qtt_14146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/02_2024/7qtt_14146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/02_2024/7qtt_14146_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtt_14146/02_2024/7qtt_14146_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 898 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 12 6.06 5 P 352 5.49 5 Mg 7 5.21 5 S 251 5.16 5 C 44800 2.51 5 N 13330 2.21 5 O 14785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 276": "OE1" <-> "OE2" Residue "O GLU 481": "OE1" <-> "OE2" Residue "O GLU 498": "OE1" <-> "OE2" Residue "V TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 73537 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 5744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 5744 Classifications: {'peptide': 1164} Incomplete info: {'truncation_to_alanine': 1014} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1103} Chain breaks: 6 Unresolved chain link angles: 60 Unresolved non-hydrogen bonds: 3591 Unresolved non-hydrogen angles: 4622 Unresolved non-hydrogen dihedrals: 2944 Unresolved non-hydrogen chiralities: 352 Planarities with less than four sites: {'GLN:plan1': 47, 'ASP:plan': 63, 'TYR:plan': 37, 'ASN:plan1': 54, 'TRP:plan': 7, 'HIS:plan': 26, 'PHE:plan': 56, 'GLU:plan': 85, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1967 Chain: "B" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 350 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 3, 'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 152 Chain: "C" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 5115 Classifications: {'peptide': 815} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 780} Unresolved non-hydrogen bonds: 1400 Unresolved non-hydrogen angles: 1735 Unresolved non-hydrogen dihedrals: 1141 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 3, 'TYR:plan': 14, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 36, 'PHE:plan': 7, 'GLU:plan': 54, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 798 Chain: "D" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 649 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 84} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1350 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 76} Link IDs: {'PTRANS': 20, 'TRANS': 177} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 138 Chain: "F" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 383 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 4, 'TRANS': 73} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 135 Chain: "G" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 364 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 533 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "L" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 177 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "N" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6157 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 36, 'TRANS': 755} Chain breaks: 4 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 184 Chain: "O" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2517 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 306} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1151 Classifications: {'peptide': 148} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "Q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "T" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1176 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "U" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2080 Classifications: {'peptide': 295} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 82} Link IDs: {'PTRANS': 17, 'TRANS': 277} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 195 Chain: "V" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1996 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 183 Chain: "W" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 2921 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 14, 'TRANS': 444} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 854 Unresolved non-hydrogen angles: 1084 Unresolved non-hydrogen dihedrals: 691 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 17, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 439 Chain: "X" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1587 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 3, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 717 Unresolved non-hydrogen dihedrals: 483 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 10, 'ASP:plan': 11, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 407 Chain: "Y" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2250 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 21, 'TRANS': 284} Chain breaks: 5 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 7, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 13, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 184 Chain: "Z" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 607 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 137 Chain: "a" Number of atoms: 15194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1936, 15194 Classifications: {'peptide': 1936} Incomplete info: {'truncation_to_alanine': 257} Link IDs: {'PCIS': 2, 'PTRANS': 103, 'TRANS': 1830} Chain breaks: 4 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 947 Unresolved non-hydrogen angles: 1218 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 14, 'TRP:plan': 6, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 28, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 515 Chain: "b" Number of atoms: 7046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7046 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 54, 'TRANS': 843} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "d" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1989 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 42, 'rna3p_pyr': 34} Link IDs: {'rna2p': 17, 'rna3p': 75} Chain breaks: 1 Chain: "e" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2070 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 11, 'rna3p_pur': 38, 'rna3p_pyr': 43} Link IDs: {'rna2p': 16, 'rna3p': 81} Chain breaks: 2 Chain: "f" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1600 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 29, 'rna3p_pyr': 41} Link IDs: {'rna2p': 6, 'rna3p': 69} Chain breaks: 3 Chain: "g" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1559 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 15, 'rna3p_pur': 24, 'rna3p_pyr': 30} Link IDs: {'rna2p': 22, 'rna3p': 53} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G%rna3p_pur:plan2': 2, ' G%rna3p_pur:plan': 2, ' U%rna3p_pyr:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "h" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 322 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "i" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 346 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "j" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 335 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Chain: "k" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 388 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "l" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 337 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "m" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 309 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "n" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 315 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'TRANS': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "p" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 776 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 9, 'TRANS': 149} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 635 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 9, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 8, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 272 Chain: "q" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 461 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 101 Chain: "u" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 1963 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 279} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1033 Unresolved non-hydrogen angles: 1324 Unresolved non-hydrogen dihedrals: 867 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 17, 'TYR:plan': 12, 'ASN:plan1': 19, 'TRP:plan': 2, 'HIS:plan': 9, 'PHE:plan': 20, 'GLU:plan': 18, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 581 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11279 SG CYS D 11 101.760 84.326 215.246 1.00231.57 S ATOM 11536 SG CYS D 46 98.680 85.210 217.853 1.00230.57 S ATOM 11559 SG CYS D 49 100.582 87.671 215.395 1.00228.78 S ATOM 11811 SG CYS D 85 98.302 84.609 214.349 1.00231.87 S ATOM 11417 SG CYS D 30 92.309 77.591 204.043 1.00196.48 S ATOM 11438 SG CYS D 33 92.992 74.491 201.835 1.00201.37 S ATOM 11727 SG CYS D 72 89.666 74.799 203.506 1.00191.16 S ATOM 11743 SG CYS D 75 92.628 74.048 205.505 1.00189.41 S ATOM 11366 SG CYS D 23 97.069 91.364 200.257 1.00220.37 S ATOM 11390 SG CYS D 26 96.978 87.711 200.449 1.00214.05 S ATOM 11631 SG CYS D 58 97.582 89.680 203.505 1.00232.39 S ATOM 11652 SG CYS D 61 100.416 89.483 200.681 1.00236.60 S ATOM 14326 SG CYS I 56 119.575 52.353 174.150 1.00176.05 S ATOM 14342 SG CYS I 59 122.920 52.425 175.983 1.00176.49 S ATOM 14635 SG CYS J 408 119.922 26.550 206.315 1.00260.71 S ATOM 14658 SG CYS J 411 121.109 24.497 203.561 1.00262.22 S ATOM 26712 SG CYS T 105 43.895 91.908 103.379 1.00124.41 S ATOM 26806 SG CYS T 117 43.909 87.990 103.513 1.00125.44 S ATOM 26820 SG CYS T 119 40.933 90.374 103.026 1.00123.86 S ATOM 26939 SG CYS T 134 43.212 89.745 106.437 1.00121.17 S ATOM 26681 SG CYS T 101 41.105 94.159 103.628 1.00122.75 S ATOM 26820 SG CYS T 119 40.933 90.374 103.026 1.00123.86 S ATOM 26972 SG CYS T 139 37.866 92.327 104.283 1.00122.74 S ATOM 26993 SG CYS T 142 39.173 93.011 100.789 1.00125.29 S ATOM 26681 SG CYS T 101 41.105 94.159 103.628 1.00122.75 S ATOM 26687 SG CYS T 102 44.178 95.450 105.509 1.00121.64 S ATOM 26712 SG CYS T 105 43.895 91.908 103.379 1.00124.41 S ATOM 26962 SG CYS T 137 41.951 93.113 106.816 1.00120.58 S ATOM 27125 SG CYS U 24 56.790 59.439 105.186 1.00153.49 S ATOM 27147 SG CYS U 27 55.512 63.179 104.600 1.00149.94 S ATOM 27590 SG CYS U 81 58.378 62.228 106.730 1.00163.48 S ATOM 27612 SG CYS U 84 54.683 61.423 107.745 1.00159.67 S ATOM 27296 SG CYS U 45 67.759 65.883 114.311 1.00147.76 S ATOM 27319 SG CYS U 48 71.447 65.743 114.674 1.00152.43 S ATOM 27515 SG CYS U 71 70.039 65.528 111.197 1.00155.85 S ATOM 27537 SG CYS U 74 69.660 62.590 113.369 1.00172.53 S ATOM 28221 SG CYS U 165 39.456 74.997 120.201 1.00122.20 S ATOM 28287 SG CYS U 173 36.704 77.323 118.905 1.00121.71 S ATOM 28335 SG CYS U 179 39.438 76.194 116.462 1.00121.79 S ATOM 37935 SG CYS Z 202 87.324 92.838 157.254 1.00118.86 S ATOM 38010 SG CYS Z 211 90.988 92.448 157.973 1.00113.72 S ATOM 38049 SG CYS Z 217 89.749 95.560 156.160 1.00107.64 S Time building chain proxies: 30.85, per 1000 atoms: 0.42 Number of scatterers: 73537 At special positions: 0 Unit cell: (211.05, 227.85, 286.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 12 29.99 S 251 16.00 P 352 15.00 Mg 7 11.99 O 14785 8.00 N 13330 7.00 C 44800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.91 Conformation dependent library (CDL) restraints added in 10.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 11 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 49 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 46 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 75 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 33 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 30 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 23 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 61 " pdb=" ZN I 600 " pdb="ZN ZN I 600 " - pdb=" NE2 HIS I 72 " pdb="ZN ZN I 600 " - pdb=" ND1 HIS I 78 " pdb="ZN ZN I 600 " - pdb=" SG CYS I 56 " pdb="ZN ZN I 600 " - pdb=" SG CYS I 59 " pdb=" ZN J1401 " pdb="ZN ZN J1401 " - pdb=" ND1 HIS J 425 " pdb="ZN ZN J1401 " - pdb=" ND1 HIS J 431 " pdb="ZN ZN J1401 " - pdb=" SG CYS J 408 " pdb="ZN ZN J1401 " - pdb=" SG CYS J 411 " pdb=" ZN T1000 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 105 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 117 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 134 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 119 " pdb=" ZN T1001 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 101 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 142 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 139 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 119 " pdb=" ZN T1002 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 101 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 137 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 102 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 105 " pdb=" ZN U 501 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 81 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 84 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 27 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 24 " pdb=" ZN U 502 " pdb="ZN ZN U 502 " - pdb=" SG CYS U 48 " pdb="ZN ZN U 502 " - pdb=" SG CYS U 71 " pdb="ZN ZN U 502 " - pdb=" SG CYS U 45 " pdb="ZN ZN U 502 " - pdb=" SG CYS U 74 " pdb=" ZN U 503 " pdb="ZN ZN U 503 " - pdb=" NE2 HIS U 183 " pdb="ZN ZN U 503 " - pdb=" SG CYS U 173 " pdb="ZN ZN U 503 " - pdb=" SG CYS U 165 " pdb="ZN ZN U 503 " - pdb=" SG CYS U 179 " pdb=" ZN Z 701 " pdb="ZN ZN Z 701 " - pdb=" NE2 HIS Z 221 " pdb="ZN ZN Z 701 " - pdb=" SG CYS Z 202 " pdb="ZN ZN Z 701 " - pdb=" SG CYS Z 211 " pdb="ZN ZN Z 701 " - pdb=" SG CYS Z 217 " Number of angles added : 57 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18428 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 321 helices and 83 sheets defined 37.3% alpha, 12.5% beta 85 base pairs and 183 stacking pairs defined. Time for finding SS restraints: 28.00 Creating SS restraints... Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 834 through 844 Processing helix chain 'A' and resid 1117 through 1133 removed outlier: 3.860A pdb=" N SER A1132 " --> pdb=" O MET A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1145 No H-bonds generated for 'chain 'A' and resid 1142 through 1145' Processing helix chain 'A' and resid 1158 through 1165 removed outlier: 3.866A pdb=" N ASN A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1178 Processing helix chain 'A' and resid 1183 through 1196 Processing helix chain 'B' and resid 12 through 15 No H-bonds generated for 'chain 'B' and resid 12 through 15' Processing helix chain 'B' and resid 28 through 45 Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 61 through 76 removed outlier: 3.607A pdb=" N LEU B 73 " --> pdb=" O MET B 69 " (cutoff:3.500A) Proline residue: B 75 - end of helix Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'C' and resid 509 through 521 Processing helix chain 'C' and resid 523 through 526 No H-bonds generated for 'chain 'C' and resid 523 through 526' Processing helix chain 'C' and resid 528 through 539 Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 546 through 567 removed outlier: 7.452A pdb=" N ASP C 565 " --> pdb=" O TYR C 561 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU C 566 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 Proline residue: C 580 - end of helix Processing helix chain 'C' and resid 587 through 603 Processing helix chain 'C' and resid 606 through 617 Proline residue: C 615 - end of helix Processing helix chain 'C' and resid 622 through 639 Processing helix chain 'C' and resid 641 through 652 Proline residue: C 646 - end of helix Processing helix chain 'C' and resid 658 through 675 Processing helix chain 'C' and resid 677 through 679 No H-bonds generated for 'chain 'C' and resid 677 through 679' Processing helix chain 'C' and resid 683 through 694 removed outlier: 4.464A pdb=" N HIS C 692 " --> pdb=" O GLU C 688 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY C 693 " --> pdb=" O ILE C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 715 Processing helix chain 'C' and resid 725 through 736 removed outlier: 4.165A pdb=" N LYS C 729 " --> pdb=" O SER C 726 " (cutoff:3.500A) Proline residue: C 730 - end of helix removed outlier: 3.845A pdb=" N ILE C 735 " --> pdb=" O TRP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 756 Proline residue: C 755 - end of helix Processing helix chain 'C' and resid 759 through 778 removed outlier: 4.403A pdb=" N LEU C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLN C 778 " --> pdb=" O ILE C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 797 Processing helix chain 'C' and resid 804 through 809 Processing helix chain 'C' and resid 811 through 817 Processing helix chain 'C' and resid 821 through 825 Processing helix chain 'C' and resid 828 through 844 Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 855 through 858 Processing helix chain 'C' and resid 862 through 878 Processing helix chain 'C' and resid 886 through 901 Processing helix chain 'C' and resid 908 through 925 removed outlier: 6.487A pdb=" N LYS C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG C 924 " --> pdb=" O ALA C 920 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL C 925 " --> pdb=" O LEU C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 941 removed outlier: 4.164A pdb=" N ASN C 941 " --> pdb=" O LEU C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 5.304A pdb=" N VAL C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL C 961 " --> pdb=" O ARG C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 983 removed outlier: 4.912A pdb=" N GLY C 983 " --> pdb=" O TYR C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 1004 Processing helix chain 'C' and resid 1013 through 1025 Proline residue: C1018 - end of helix Proline residue: C1022 - end of helix removed outlier: 4.450A pdb=" N LYS C1025 " --> pdb=" O THR C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1045 Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1052 through 1067 removed outlier: 3.877A pdb=" N GLU C1064 " --> pdb=" O PHE C1060 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1071 through 1088 Processing helix chain 'C' and resid 1092 through 1101 Processing helix chain 'C' and resid 1110 through 1122 Processing helix chain 'C' and resid 1126 through 1137 Proline residue: C1130 - end of helix removed outlier: 3.727A pdb=" N TYR C1136 " --> pdb=" O LEU C1132 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG C1137 " --> pdb=" O MET C1133 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1164 removed outlier: 7.223A pdb=" N GLU C1160 " --> pdb=" O GLU C1156 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N MET C1161 " --> pdb=" O TYR C1157 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY C1162 " --> pdb=" O ILE C1158 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LYS C1163 " --> pdb=" O GLY C1159 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP C1164 " --> pdb=" O GLU C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1177 Proline residue: C1171 - end of helix Processing helix chain 'C' and resid 1182 through 1198 Processing helix chain 'C' and resid 1205 through 1220 removed outlier: 3.731A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) Proline residue: C1217 - end of helix removed outlier: 5.663A pdb=" N PHE C1220 " --> pdb=" O TRP C1216 " (cutoff:3.500A) Processing helix chain 'C' and resid 1224 through 1240 Processing helix chain 'C' and resid 1243 through 1251 Processing helix chain 'C' and resid 1259 through 1275 Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 80 through 83 Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 479 through 481 No H-bonds generated for 'chain 'E' and resid 479 through 481' Processing helix chain 'E' and resid 485 through 492 Processing helix chain 'E' and resid 502 through 504 No H-bonds generated for 'chain 'E' and resid 502 through 504' Processing helix chain 'E' and resid 526 through 531 Processing helix chain 'E' and resid 533 through 545 Processing helix chain 'E' and resid 549 through 557 Processing helix chain 'E' and resid 569 through 575 Processing helix chain 'E' and resid 611 through 616 Processing helix chain 'E' and resid 633 through 638 Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 64 through 72 Processing helix chain 'F' and resid 79 through 81 No H-bonds generated for 'chain 'F' and resid 79 through 81' Processing helix chain 'G' and resid 102 through 135 removed outlier: 3.914A pdb=" N LYS G 106 " --> pdb=" O SER G 102 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP G 125 " --> pdb=" O ASN G 121 " (cutoff:3.500A) Proline residue: G 126 - end of helix Proline residue: G 131 - end of helix Processing helix chain 'G' and resid 167 through 175 Processing helix chain 'I' and resid 19 through 41 Processing helix chain 'I' and resid 66 through 70 Processing helix chain 'I' and resid 78 through 86 Processing helix chain 'J' and resid 395 through 398 No H-bonds generated for 'chain 'J' and resid 395 through 398' Processing helix chain 'J' and resid 419 through 424 Processing helix chain 'J' and resid 430 through 438 Processing helix chain 'J' and resid 445 through 447 No H-bonds generated for 'chain 'J' and resid 445 through 447' Processing helix chain 'J' and resid 453 through 457 Processing helix chain 'L' and resid 531 through 539 Processing helix chain 'L' and resid 544 through 556 Processing helix chain 'N' and resid 162 through 192 Processing helix chain 'N' and resid 224 through 256 removed outlier: 4.452A pdb=" N GLU N 248 " --> pdb=" O LEU N 244 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA N 249 " --> pdb=" O GLU N 245 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 295 Processing helix chain 'N' and resid 325 through 337 Processing helix chain 'N' and resid 385 through 397 Processing helix chain 'N' and resid 405 through 414 Processing helix chain 'N' and resid 428 through 437 Proline residue: N 433 - end of helix Processing helix chain 'N' and resid 455 through 469 Processing helix chain 'N' and resid 498 through 507 Processing helix chain 'N' and resid 527 through 542 Processing helix chain 'N' and resid 558 through 563 Processing helix chain 'N' and resid 593 through 604 Processing helix chain 'N' and resid 618 through 633 removed outlier: 3.705A pdb=" N ALA N 623 " --> pdb=" O GLU N 619 " (cutoff:3.500A) Processing helix chain 'N' and resid 653 through 657 Processing helix chain 'N' and resid 676 through 679 No H-bonds generated for 'chain 'N' and resid 676 through 679' Processing helix chain 'N' and resid 716 through 726 Processing helix chain 'N' and resid 740 through 744 Processing helix chain 'N' and resid 754 through 757 No H-bonds generated for 'chain 'N' and resid 754 through 757' Processing helix chain 'N' and resid 761 through 769 removed outlier: 4.499A pdb=" N LEU N 765 " --> pdb=" O GLY N 761 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU N 766 " --> pdb=" O ASN N 762 " (cutoff:3.500A) Processing helix chain 'N' and resid 786 through 798 Processing helix chain 'N' and resid 810 through 817 Processing helix chain 'N' and resid 822 through 830 removed outlier: 5.058A pdb=" N MET N 827 " --> pdb=" O MET N 823 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE N 828 " --> pdb=" O LEU N 824 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU N 829 " --> pdb=" O SER N 825 " (cutoff:3.500A) Processing helix chain 'N' and resid 837 through 847 Processing helix chain 'N' and resid 862 through 871 removed outlier: 3.866A pdb=" N PHE N 871 " --> pdb=" O ALA N 867 " (cutoff:3.500A) Processing helix chain 'N' and resid 876 through 888 removed outlier: 3.949A pdb=" N VAL N 880 " --> pdb=" O GLY N 876 " (cutoff:3.500A) Processing helix chain 'N' and resid 895 through 900 Processing helix chain 'N' and resid 908 through 922 removed outlier: 3.836A pdb=" N LEU N 922 " --> pdb=" O LEU N 918 " (cutoff:3.500A) Processing helix chain 'N' and resid 936 through 946 Processing helix chain 'P' and resid 13 through 26 Processing helix chain 'P' and resid 32 through 35 No H-bonds generated for 'chain 'P' and resid 32 through 35' Processing helix chain 'P' and resid 43 through 52 Processing helix chain 'P' and resid 65 through 77 Processing helix chain 'P' and resid 82 through 89 Proline residue: P 87 - end of helix Processing helix chain 'P' and resid 93 through 107 Processing helix chain 'P' and resid 171 through 189 Processing helix chain 'Q' and resid 32 through 34 No H-bonds generated for 'chain 'Q' and resid 32 through 34' Processing helix chain 'Q' and resid 51 through 54 No H-bonds generated for 'chain 'Q' and resid 51 through 54' Processing helix chain 'Q' and resid 59 through 74 Processing helix chain 'Q' and resid 204 through 208 removed outlier: 3.967A pdb=" N ASP Q 207 " --> pdb=" O GLN Q 204 " (cutoff:3.500A) Processing helix chain 'Q' and resid 218 through 227 Processing helix chain 'T' and resid 13 through 15 No H-bonds generated for 'chain 'T' and resid 13 through 15' Processing helix chain 'T' and resid 19 through 34 Processing helix chain 'T' and resid 47 through 64 removed outlier: 3.965A pdb=" N ARG T 51 " --> pdb=" O TRP T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 80 Processing helix chain 'T' and resid 86 through 92 Processing helix chain 'T' and resid 104 through 106 No H-bonds generated for 'chain 'T' and resid 104 through 106' Processing helix chain 'T' and resid 123 through 125 No H-bonds generated for 'chain 'T' and resid 123 through 125' Processing helix chain 'U' and resid 25 through 28 No H-bonds generated for 'chain 'U' and resid 25 through 28' Processing helix chain 'U' and resid 72 through 78 Processing helix chain 'U' and resid 94 through 100 Processing helix chain 'U' and resid 111 through 126 Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 166 through 169 No H-bonds generated for 'chain 'U' and resid 166 through 169' Processing helix chain 'U' and resid 176 through 178 No H-bonds generated for 'chain 'U' and resid 176 through 178' Processing helix chain 'U' and resid 192 through 194 No H-bonds generated for 'chain 'U' and resid 192 through 194' Processing helix chain 'U' and resid 198 through 203 Processing helix chain 'U' and resid 208 through 218 Processing helix chain 'U' and resid 245 through 252 Processing helix chain 'U' and resid 277 through 286 Processing helix chain 'V' and resid 22 through 33 Processing helix chain 'V' and resid 133 through 140 Processing helix chain 'V' and resid 205 through 227 Processing helix chain 'V' and resid 253 through 262 removed outlier: 4.120A pdb=" N ARG V 262 " --> pdb=" O ILE V 258 " (cutoff:3.500A) Processing helix chain 'V' and resid 291 through 300 removed outlier: 3.728A pdb=" N LYS V 300 " --> pdb=" O LYS V 296 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 171 Processing helix chain 'W' and resid 178 through 187 Processing helix chain 'W' and resid 194 through 207 Processing helix chain 'W' and resid 210 through 225 removed outlier: 3.971A pdb=" N HIS W 213 " --> pdb=" O ILE W 210 " (cutoff:3.500A) Processing helix chain 'W' and resid 227 through 246 Processing helix chain 'W' and resid 250 through 265 Processing helix chain 'W' and resid 271 through 283 Processing helix chain 'W' and resid 287 through 299 Processing helix chain 'W' and resid 301 through 307 Processing helix chain 'W' and resid 309 through 323 Processing helix chain 'W' and resid 330 through 345 Processing helix chain 'W' and resid 391 through 405 Processing helix chain 'W' and resid 451 through 465 Processing helix chain 'W' and resid 469 through 478 Processing helix chain 'W' and resid 483 through 498 removed outlier: 3.951A pdb=" N THR W 486 " --> pdb=" O GLU W 483 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS W 487 " --> pdb=" O SER W 484 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU W 488 " --> pdb=" O GLN W 485 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP W 495 " --> pdb=" O MET W 492 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA W 498 " --> pdb=" O ASP W 495 " (cutoff:3.500A) Processing helix chain 'W' and resid 505 through 517 Processing helix chain 'W' and resid 519 through 534 Processing helix chain 'W' and resid 541 through 556 Processing helix chain 'W' and resid 562 through 567 Processing helix chain 'W' and resid 577 through 593 Processing helix chain 'W' and resid 596 through 603 Processing helix chain 'W' and resid 621 through 634 Processing helix chain 'W' and resid 641 through 648 Processing helix chain 'X' and resid 217 through 237 Processing helix chain 'X' and resid 242 through 254 Processing helix chain 'X' and resid 258 through 271 Processing helix chain 'X' and resid 276 through 288 Processing helix chain 'X' and resid 292 through 305 Processing helix chain 'X' and resid 310 through 321 Processing helix chain 'X' and resid 327 through 338 Processing helix chain 'X' and resid 343 through 355 Processing helix chain 'X' and resid 360 through 372 Processing helix chain 'X' and resid 376 through 388 Processing helix chain 'X' and resid 392 through 405 Processing helix chain 'X' and resid 415 through 426 Processing helix chain 'X' and resid 428 through 441 Processing helix chain 'X' and resid 449 through 460 Processing helix chain 'Y' and resid 98 through 102 Processing helix chain 'Y' and resid 116 through 118 No H-bonds generated for 'chain 'Y' and resid 116 through 118' Processing helix chain 'Y' and resid 137 through 162 Processing helix chain 'Y' and resid 239 through 244 Processing helix chain 'Y' and resid 286 through 336 Processing helix chain 'Y' and resid 353 through 372 Processing helix chain 'Y' and resid 378 through 381 No H-bonds generated for 'chain 'Y' and resid 378 through 381' Processing helix chain 'Y' and resid 389 through 393 Processing helix chain 'Z' and resid 203 through 206 No H-bonds generated for 'chain 'Z' and resid 203 through 206' Processing helix chain 'Z' and resid 214 through 216 No H-bonds generated for 'chain 'Z' and resid 214 through 216' Processing helix chain 'Z' and resid 229 through 234 Processing helix chain 'Z' and resid 283 through 292 Processing helix chain 'a' and resid 63 through 71 Processing helix chain 'a' and resid 74 through 76 No H-bonds generated for 'chain 'a' and resid 74 through 76' Processing helix chain 'a' and resid 85 through 92 removed outlier: 3.966A pdb=" N ALA a 91 " --> pdb=" O VAL a 87 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU a 92 " --> pdb=" O TYR a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 95 through 105 removed outlier: 3.866A pdb=" N ASN a 105 " --> pdb=" O LYS a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 137 through 157 Processing helix chain 'a' and resid 178 through 181 No H-bonds generated for 'chain 'a' and resid 178 through 181' Processing helix chain 'a' and resid 232 through 241 Processing helix chain 'a' and resid 252 through 254 No H-bonds generated for 'chain 'a' and resid 252 through 254' Processing helix chain 'a' and resid 260 through 268 Processing helix chain 'a' and resid 295 through 297 No H-bonds generated for 'chain 'a' and resid 295 through 297' Processing helix chain 'a' and resid 310 through 315 Processing helix chain 'a' and resid 398 through 405 Processing helix chain 'a' and resid 409 through 411 No H-bonds generated for 'chain 'a' and resid 409 through 411' Processing helix chain 'a' and resid 428 through 432 Processing helix chain 'a' and resid 441 through 459 Processing helix chain 'a' and resid 472 through 477 Processing helix chain 'a' and resid 489 through 510 Processing helix chain 'a' and resid 532 through 537 Processing helix chain 'a' and resid 542 through 565 Processing helix chain 'a' and resid 571 through 583 Processing helix chain 'a' and resid 585 through 588 No H-bonds generated for 'chain 'a' and resid 585 through 588' Processing helix chain 'a' and resid 591 through 593 No H-bonds generated for 'chain 'a' and resid 591 through 593' Processing helix chain 'a' and resid 596 through 616 Processing helix chain 'a' and resid 631 through 660 Proline residue: a 646 - end of helix Processing helix chain 'a' and resid 678 through 694 Processing helix chain 'a' and resid 706 through 721 Processing helix chain 'a' and resid 733 through 763 Processing helix chain 'a' and resid 769 through 797 Processing helix chain 'a' and resid 804 through 819 Processing helix chain 'a' and resid 835 through 847 Processing helix chain 'a' and resid 858 through 872 Processing helix chain 'a' and resid 874 through 887 Processing helix chain 'a' and resid 913 through 932 Processing helix chain 'a' and resid 948 through 960 Processing helix chain 'a' and resid 985 through 987 No H-bonds generated for 'chain 'a' and resid 985 through 987' Processing helix chain 'a' and resid 990 through 999 removed outlier: 3.806A pdb=" N LEU a 999 " --> pdb=" O ARG a 995 " (cutoff:3.500A) Processing helix chain 'a' and resid 1003 through 1013 removed outlier: 3.945A pdb=" N ASN a1013 " --> pdb=" O MET a1009 " (cutoff:3.500A) Processing helix chain 'a' and resid 1037 through 1053 Processing helix chain 'a' and resid 1055 through 1062 Processing helix chain 'a' and resid 1077 through 1080 No H-bonds generated for 'chain 'a' and resid 1077 through 1080' Processing helix chain 'a' and resid 1103 through 1116 Processing helix chain 'a' and resid 1144 through 1160 removed outlier: 3.687A pdb=" N ARG a1160 " --> pdb=" O ASP a1156 " (cutoff:3.500A) Processing helix chain 'a' and resid 1234 through 1253 removed outlier: 4.672A pdb=" N GLY a1252 " --> pdb=" O LEU a1248 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N SER a1253 " --> pdb=" O MET a1249 " (cutoff:3.500A) Processing helix chain 'a' and resid 1256 through 1278 removed outlier: 7.468A pdb=" N GLU a1276 " --> pdb=" O THR a1272 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA a1277 " --> pdb=" O TYR a1273 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL a1278 " --> pdb=" O PHE a1274 " (cutoff:3.500A) Processing helix chain 'a' and resid 1282 through 1302 Processing helix chain 'a' and resid 1313 through 1317 removed outlier: 4.077A pdb=" N TYR a1317 " --> pdb=" O VAL a1314 " (cutoff:3.500A) Processing helix chain 'a' and resid 1320 through 1322 No H-bonds generated for 'chain 'a' and resid 1320 through 1322' Processing helix chain 'a' and resid 1369 through 1371 No H-bonds generated for 'chain 'a' and resid 1369 through 1371' Processing helix chain 'a' and resid 1375 through 1398 Processing helix chain 'a' and resid 1405 through 1408 No H-bonds generated for 'chain 'a' and resid 1405 through 1408' Processing helix chain 'a' and resid 1419 through 1423 Processing helix chain 'a' and resid 1427 through 1430 No H-bonds generated for 'chain 'a' and resid 1427 through 1430' Processing helix chain 'a' and resid 1437 through 1445 removed outlier: 5.265A pdb=" N TYR a1445 " --> pdb=" O ASP a1441 " (cutoff:3.500A) Processing helix chain 'a' and resid 1468 through 1477 removed outlier: 3.887A pdb=" N THR a1472 " --> pdb=" O ASN a1468 " (cutoff:3.500A) Processing helix chain 'a' and resid 1480 through 1487 removed outlier: 4.300A pdb=" N HIS a1487 " --> pdb=" O GLY a1483 " (cutoff:3.500A) Processing helix chain 'a' and resid 1491 through 1493 No H-bonds generated for 'chain 'a' and resid 1491 through 1493' Processing helix chain 'a' and resid 1528 through 1537 Processing helix chain 'a' and resid 1539 through 1542 No H-bonds generated for 'chain 'a' and resid 1539 through 1542' Processing helix chain 'a' and resid 1567 through 1576 Processing helix chain 'a' and resid 1581 through 1599 Processing helix chain 'a' and resid 1602 through 1604 No H-bonds generated for 'chain 'a' and resid 1602 through 1604' Processing helix chain 'a' and resid 1616 through 1618 No H-bonds generated for 'chain 'a' and resid 1616 through 1618' Processing helix chain 'a' and resid 1677 through 1688 Processing helix chain 'a' and resid 1722 through 1736 Processing helix chain 'a' and resid 1738 through 1751 Processing helix chain 'a' and resid 1767 through 1770 No H-bonds generated for 'chain 'a' and resid 1767 through 1770' Processing helix chain 'a' and resid 1836 through 1851 Processing helix chain 'a' and resid 1870 through 1874 Processing helix chain 'a' and resid 1893 through 1895 No H-bonds generated for 'chain 'a' and resid 1893 through 1895' Processing helix chain 'a' and resid 1900 through 1907 Processing helix chain 'a' and resid 1929 through 1945 Processing helix chain 'a' and resid 1947 through 1954 Processing helix chain 'a' and resid 1958 through 1960 No H-bonds generated for 'chain 'a' and resid 1958 through 1960' Processing helix chain 'a' and resid 1973 through 1994 Processing helix chain 'a' and resid 2004 through 2012 Processing helix chain 'b' and resid 69 through 73 Processing helix chain 'b' and resid 116 through 124 removed outlier: 4.237A pdb=" N ASP b 124 " --> pdb=" O ALA b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 142 through 153 Processing helix chain 'b' and resid 172 through 177 Processing helix chain 'b' and resid 209 through 221 removed outlier: 4.886A pdb=" N ASP b 213 " --> pdb=" O ASN b 210 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 248 Processing helix chain 'b' and resid 260 through 264 Processing helix chain 'b' and resid 271 through 292 Processing helix chain 'b' and resid 320 through 330 Processing helix chain 'b' and resid 336 through 343 Processing helix chain 'b' and resid 368 through 372 Processing helix chain 'b' and resid 374 through 386 Processing helix chain 'b' and resid 392 through 398 Processing helix chain 'b' and resid 412 through 424 Processing helix chain 'b' and resid 429 through 437 Processing helix chain 'b' and resid 441 through 452 removed outlier: 5.349A pdb=" N LYS b 446 " --> pdb=" O LYS b 442 " (cutoff:3.500A) Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 460 through 466 Processing helix chain 'b' and resid 597 through 613 Proline residue: b 601 - end of helix Processing helix chain 'b' and resid 634 through 646 Processing helix chain 'b' and resid 695 through 701 Processing helix chain 'b' and resid 711 through 722 removed outlier: 3.962A pdb=" N LYS b 721 " --> pdb=" O PHE b 717 " (cutoff:3.500A) Processing helix chain 'b' and resid 726 through 731 Processing helix chain 'b' and resid 756 through 761 Processing helix chain 'b' and resid 763 through 776 Processing helix chain 'b' and resid 807 through 821 removed outlier: 3.733A pdb=" N THR b 811 " --> pdb=" O GLN b 807 " (cutoff:3.500A) Processing helix chain 'b' and resid 840 through 852 removed outlier: 3.736A pdb=" N VAL b 843 " --> pdb=" O ALA b 840 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER b 844 " --> pdb=" O ASP b 841 " (cutoff:3.500A) Processing helix chain 'b' and resid 883 through 890 Processing helix chain 'b' and resid 926 through 941 removed outlier: 4.934A pdb=" N ALA b 930 " --> pdb=" O PRO b 927 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG b 931 " --> pdb=" O HIS b 928 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS b 936 " --> pdb=" O PHE b 933 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS b 941 " --> pdb=" O ARG b 938 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 13 Processing helix chain 'i' and resid 17 through 27 Processing helix chain 'j' and resid 6 through 12 Processing helix chain 'k' and resid 3 through 9 Processing helix chain 'l' and resid 28 through 39 Processing helix chain 'm' and resid 22 through 24 No H-bonds generated for 'chain 'm' and resid 22 through 24' Processing helix chain 'p' and resid 33 through 45 Processing helix chain 'p' and resid 136 through 143 Processing helix chain 'q' and resid 55 through 71 removed outlier: 3.504A pdb=" N LYS q 63 " --> pdb=" O ASP q 59 " (cutoff:3.500A) Processing helix chain 'q' and resid 82 through 99 Processing helix chain 'u' and resid 63 through 68 Proline residue: u 68 - end of helix Processing helix chain 'u' and resid 128 through 136 Processing helix chain 'u' and resid 202 through 214 Processing helix chain 'u' and resid 235 through 237 No H-bonds generated for 'chain 'u' and resid 235 through 237' Processing helix chain 'u' and resid 245 through 251 Processing helix chain 'u' and resid 301 through 312 Processing helix chain 'u' and resid 404 through 411 Processing helix chain 'u' and resid 437 through 452 removed outlier: 4.079A pdb=" N GLN u 452 " --> pdb=" O GLU u 448 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 1155 through 1157 removed outlier: 6.250A pdb=" N LEU A 3 " --> pdb=" O ILE A1156 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A1112 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A1108 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A1099 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.790A pdb=" N PHE A 16 " --> pdb=" O SER A 33 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 62 through 69 removed outlier: 7.188A pdb=" N GLY A 81 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU A 65 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA A 67 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR A 77 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP A 76 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR A 92 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 88 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER A 82 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU A 91 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS A 101 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN A 93 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE A 99 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 120 through 123 Processing sheet with id= E, first strand: chain 'A' and resid 165 through 167 removed outlier: 5.903A pdb=" N GLU A 212 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG A 222 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP A 214 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL A 220 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 170 through 173 removed outlier: 4.638A pdb=" N MET A 181 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 234 through 238 removed outlier: 3.886A pdb=" N PHE A 234 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS A 251 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY A 247 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 290 through 294 removed outlier: 5.862A pdb=" N LYS A 312 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR A 329 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 336 through 342 removed outlier: 6.991A pdb=" N ALA A 350 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET A 339 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE A 348 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL A 341 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE A 346 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN A 360 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU A 397 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 775 through 780 removed outlier: 6.383A pdb=" N GLY A 428 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 407 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 458 through 461 Processing sheet with id= L, first strand: chain 'A' and resid 533 through 536 Processing sheet with id= M, first strand: chain 'A' and resid 574 through 576 Processing sheet with id= N, first strand: chain 'A' and resid 587 through 592 removed outlier: 7.104A pdb=" N GLY A 608 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N MET A 590 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ALA A 606 " --> pdb=" O MET A 590 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 687 through 689 Processing sheet with id= P, first strand: chain 'A' and resid 703 through 706 removed outlier: 4.315A pdb=" N GLU A 710 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP A 720 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 721 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR A 732 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 741 through 745 removed outlier: 3.638A pdb=" N THR A 761 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 785 through 790 removed outlier: 7.208A pdb=" N ILE A 800 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE A 788 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 798 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 868 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP A 878 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 886 through 890 removed outlier: 6.374A pdb=" N GLY A 908 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 922 " --> pdb=" O LYS A 911 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 951 through 954 removed outlier: 3.984A pdb=" N ALA A 951 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 992 through 995 removed outlier: 3.954A pdb=" N GLY A 992 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG A1013 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE A1023 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LYS A1015 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU A1021 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 1043 through 1047 removed outlier: 6.165A pdb=" N ARG A1057 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL A1073 " --> pdb=" O ARG A1057 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.241A pdb=" N TYR D 71 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 85 through 88 Processing sheet with id= Y, first strand: chain 'I' and resid 46 through 48 removed outlier: 3.819A pdb=" N TYR I 54 " --> pdb=" O HIS I 63 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 405 through 408 Processing sheet with id= AA, first strand: chain 'N' and resid 548 through 550 removed outlier: 3.654A pdb=" N LEU N 418 " --> pdb=" O VAL N 548 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL N 550 " --> pdb=" O LEU N 418 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 448 through 452 removed outlier: 4.085A pdb=" N THR N 497 " --> pdb=" O SER N 480 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 670 through 673 removed outlier: 6.487A pdb=" N ILE N 611 " --> pdb=" O VAL N 671 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA N 673 " --> pdb=" O ILE N 611 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL N 613 " --> pdb=" O ALA N 673 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU N 612 " --> pdb=" O ILE N 687 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL N 689 " --> pdb=" O LEU N 612 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE N 614 " --> pdb=" O VAL N 689 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 694 through 701 Processing sheet with id= AE, first strand: chain 'N' and resid 983 through 985 removed outlier: 3.829A pdb=" N TRP N 983 " --> pdb=" O ILE N1003 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'O' and resid 207 through 212 removed outlier: 6.775A pdb=" N GLY O 222 " --> pdb=" O ARG O 208 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE O 210 " --> pdb=" O VAL O 220 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL O 220 " --> pdb=" O ILE O 210 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL O 212 " --> pdb=" O TRP O 218 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TRP O 218 " --> pdb=" O VAL O 212 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR O 227 " --> pdb=" O SER O 223 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP O 232 " --> pdb=" O LEU O 238 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU O 238 " --> pdb=" O ASP O 232 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'O' and resid 249 through 254 removed outlier: 6.748A pdb=" N CYS O 264 " --> pdb=" O ARG O 250 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL O 252 " --> pdb=" O PHE O 262 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE O 262 " --> pdb=" O VAL O 252 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL O 254 " --> pdb=" O TYR O 260 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR O 260 " --> pdb=" O VAL O 254 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY O 265 " --> pdb=" O GLN O 269 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLN O 269 " --> pdb=" O GLY O 265 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP O 274 " --> pdb=" O VAL O 280 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL O 280 " --> pdb=" O ASP O 274 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'O' and resid 291 through 296 removed outlier: 6.813A pdb=" N CYS O 306 " --> pdb=" O TYR O 292 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU O 294 " --> pdb=" O VAL O 304 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL O 304 " --> pdb=" O LEU O 294 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU O 296 " --> pdb=" O VAL O 302 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL O 302 " --> pdb=" O LEU O 296 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR O 311 " --> pdb=" O SER O 307 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP O 316 " --> pdb=" O SER O 322 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER O 322 " --> pdb=" O ASP O 316 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 333 through 338 removed outlier: 7.079A pdb=" N GLY O 348 " --> pdb=" O ALA O 334 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL O 336 " --> pdb=" O ILE O 346 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE O 346 " --> pdb=" O VAL O 336 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE O 345 " --> pdb=" O TRP O 357 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 375 through 380 removed outlier: 6.736A pdb=" N GLY O 390 " --> pdb=" O ARG O 376 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL O 378 " --> pdb=" O ALA O 388 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA O 388 " --> pdb=" O VAL O 378 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU O 380 " --> pdb=" O THR O 386 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR O 386 " --> pdb=" O LEU O 380 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE O 387 " --> pdb=" O TRP O 398 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS O 399 " --> pdb=" O PHE O 405 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE O 405 " --> pdb=" O LYS O 399 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 416 through 421 removed outlier: 7.039A pdb=" N GLY O 430 " --> pdb=" O ASN O 417 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU O 419 " --> pdb=" O VAL O 428 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL O 428 " --> pdb=" O LEU O 419 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL O 421 " --> pdb=" O VAL O 426 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL O 426 " --> pdb=" O VAL O 421 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR O 435 " --> pdb=" O ALA O 431 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN O 448 " --> pdb=" O LEU O 438 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP O 440 " --> pdb=" O ASN O 446 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN O 446 " --> pdb=" O ASP O 440 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'O' and resid 194 through 201 removed outlier: 7.088A pdb=" N VAL O 488 " --> pdb=" O TYR O 197 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL O 199 " --> pdb=" O ILE O 486 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE O 486 " --> pdb=" O VAL O 199 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR O 485 " --> pdb=" O GLU O 481 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA O 467 " --> pdb=" O ALA O 480 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'U' and resid 36 through 39 Processing sheet with id= AN, first strand: chain 'U' and resid 299 through 302 Processing sheet with id= AO, first strand: chain 'U' and resid 291 through 293 removed outlier: 4.178A pdb=" N LEU U 291 " --> pdb=" O LEU U 298 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'V' and resid 156 through 161 removed outlier: 7.132A pdb=" N GLU V 6 " --> pdb=" O ASN V 157 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR V 159 " --> pdb=" O LEU V 4 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU V 4 " --> pdb=" O THR V 159 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ASP V 15 " --> pdb=" O VAL V 129 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL V 129 " --> pdb=" O ASP V 15 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL V 94 " --> pdb=" O PHE V 126 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR V 93 " --> pdb=" O THR V 111 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'V' and resid 312 through 315 Processing sheet with id= AR, first strand: chain 'Y' and resid 175 through 179 Processing sheet with id= AS, first strand: chain 'Z' and resid 272 through 274 Processing sheet with id= AT, first strand: chain 'a' and resid 482 through 488 Processing sheet with id= AU, first strand: chain 'a' and resid 227 through 229 Processing sheet with id= AV, first strand: chain 'a' and resid 895 through 900 Processing sheet with id= AW, first strand: chain 'a' and resid 1174 through 1178 removed outlier: 6.584A pdb=" N ARG a1100 " --> pdb=" O ILE a1085 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE a1085 " --> pdb=" O ARG a1100 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'a' and resid 1016 through 1019 Processing sheet with id= AY, first strand: chain 'a' and resid 1184 through 1189 removed outlier: 6.844A pdb=" N LEU a1216 " --> pdb=" O THR a1225 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN a1227 " --> pdb=" O TRP a1214 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TRP a1214 " --> pdb=" O GLN a1227 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'a' and resid 1335 through 1337 Processing sheet with id= BA, first strand: chain 'a' and resid 1552 through 1554 Processing sheet with id= BB, first strand: chain 'a' and resid 1711 through 1716 removed outlier: 6.408A pdb=" N TRP a1661 " --> pdb=" O VAL a1701 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE a1703 " --> pdb=" O TRP a1661 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP a1663 " --> pdb=" O ILE a1703 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE a1705 " --> pdb=" O ASP a1663 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN a1665 " --> pdb=" O ILE a1705 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'a' and resid 1637 through 1639 Processing sheet with id= BD, first strand: chain 'a' and resid 1778 through 1781 removed outlier: 3.504A pdb=" N GLN a1816 " --> pdb=" O ASN a1811 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'a' and resid 1861 through 1863 Processing sheet with id= BF, first strand: chain 'b' and resid 316 through 318 removed outlier: 9.582A pdb=" N CYS b 308 " --> pdb=" O VAL b 253 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL b 255 " --> pdb=" O CYS b 308 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER b 310 " --> pdb=" O VAL b 255 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE b 257 " --> pdb=" O SER b 310 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ARG b 130 " --> pdb=" O SER b 197 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU b 199 " --> pdb=" O ARG b 130 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL b 132 " --> pdb=" O LEU b 199 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ASN b 201 " --> pdb=" O VAL b 132 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU b 134 " --> pdb=" O ASN b 201 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N MET b 203 " --> pdb=" O LEU b 134 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY b 136 " --> pdb=" O MET b 203 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'b' and resid 348 through 350 Processing sheet with id= BH, first strand: chain 'b' and resid 523 through 525 removed outlier: 6.974A pdb=" N HIS b 477 " --> pdb=" O VAL b 496 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL b 496 " --> pdb=" O HIS b 477 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'b' and resid 480 through 483 removed outlier: 3.614A pdb=" N LYS b 480 " --> pdb=" O PHE b 493 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'b' and resid 530 through 533 removed outlier: 3.973A pdb=" N LEU b 530 " --> pdb=" O VAL b 541 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'b' and resid 653 through 655 removed outlier: 3.895A pdb=" N HIS b 627 " --> pdb=" O VAL b 592 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR b 618 " --> pdb=" O LEU b 630 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'b' and resid 663 through 665 removed outlier: 3.586A pdb=" N HIS b 903 " --> pdb=" O TYR b 831 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE b 833 " --> pdb=" O PHE b 901 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE b 901 " --> pdb=" O PHE b 833 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLU b 835 " --> pdb=" O SER b 899 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER b 899 " --> pdb=" O GLU b 835 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLN b 837 " --> pdb=" O SER b 897 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N SER b 897 " --> pdb=" O GLN b 837 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'b' and resid 675 through 677 removed outlier: 6.138A pdb=" N ILE b 688 " --> pdb=" O ILE b 791 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE b 791 " --> pdb=" O ILE b 688 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU b 690 " --> pdb=" O PHE b 789 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE b 789 " --> pdb=" O GLU b 690 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA b 734 " --> pdb=" O LEU b 745 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP b 747 " --> pdb=" O ILE b 732 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE b 732 " --> pdb=" O ASP b 747 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'b' and resid 831 through 838 removed outlier: 6.482A pdb=" N PHE b 874 " --> pdb=" O VAL b 857 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL b 857 " --> pdb=" O PHE b 874 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'h' and resid 57 through 60 removed outlier: 3.558A pdb=" N LEU h 59 " --> pdb=" O THR h 47 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR h 47 " --> pdb=" O LEU h 59 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'h' and resid 32 through 36 removed outlier: 6.728A pdb=" N GLN h 43 " --> pdb=" O VAL h 34 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'i' and resid 62 through 64 removed outlier: 8.811A pdb=" N ASN i 40 " --> pdb=" O VAL i 33 " (cutoff:3.500A) removed outlier: 11.259A pdb=" N VAL i 33 " --> pdb=" O ASN i 40 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N ARG i 42 " --> pdb=" O ILE i 31 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N ILE i 31 " --> pdb=" O ARG i 42 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU i 86 " --> pdb=" O TRP i 34 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'i' and resid 76 through 79 removed outlier: 3.671A pdb=" N ILE i 77 " --> pdb=" O LEU i 58 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP i 59 " --> pdb=" O ILE i 47 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE i 47 " --> pdb=" O ASP i 59 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'j' and resid 68 through 71 removed outlier: 6.905A pdb=" N GLU j 21 " --> pdb=" O ARG j 69 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU j 71 " --> pdb=" O THR j 19 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR j 19 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN j 42 " --> pdb=" O ILE j 33 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'j' and resid 46 through 48 Processing sheet with id= BU, first strand: chain 'k' and resid 52 through 55 removed outlier: 3.762A pdb=" N HIS k 26 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN k 24 " --> pdb=" O THR k 46 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'k' and resid 57 through 59 removed outlier: 3.544A pdb=" N GLY k 31 " --> pdb=" O HIS k 39 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS k 41 " --> pdb=" O ILE k 29 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE k 29 " --> pdb=" O LYS k 41 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'l' and resid 94 through 96 Processing sheet with id= BX, first strand: chain 'l' and resid 98 through 101 removed outlier: 6.127A pdb=" N GLU l 68 " --> pdb=" O VAL l 56 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL l 56 " --> pdb=" O GLU l 68 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'm' and resid 67 through 71 removed outlier: 3.514A pdb=" N ILE m 68 " --> pdb=" O LYS m 20 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS m 20 " --> pdb=" O ILE m 68 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU m 70 " --> pdb=" O SER m 18 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER m 18 " --> pdb=" O LEU m 70 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL m 41 " --> pdb=" O ARG m 32 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'n' and resid 77 through 82 removed outlier: 7.119A pdb=" N ILE n 20 " --> pdb=" O VAL n 78 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET n 80 " --> pdb=" O ARG n 18 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG n 18 " --> pdb=" O MET n 80 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL n 82 " --> pdb=" O ARG n 16 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ARG n 16 " --> pdb=" O VAL n 82 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE n 41 " --> pdb=" O LYS n 32 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'p' and resid 22 through 26 Processing sheet with id= CB, first strand: chain 'p' and resid 62 through 64 Processing sheet with id= CC, first strand: chain 'u' and resid 52 through 54 Processing sheet with id= CD, first strand: chain 'u' and resid 125 through 127 Processing sheet with id= CE, first strand: chain 'u' and resid 329 through 332 removed outlier: 6.039A pdb=" N MET u 368 " --> pdb=" O ILE u 396 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE u 396 " --> pdb=" O MET u 368 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG u 283 " --> pdb=" O VAL u 433 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL u 433 " --> pdb=" O ARG u 283 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS u 285 " --> pdb=" O THR u 431 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR u 431 " --> pdb=" O HIS u 285 " (cutoff:3.500A) 3007 hydrogen bonds defined for protein. 8271 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 207 hydrogen bonds 350 hydrogen bond angles 0 basepair planarities 85 basepair parallelities 183 stacking parallelities Total time for adding SS restraints: 42.75 Time building geometry restraints manager: 26.09 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: 23325 1.34 - 1.46: 19423 1.46 - 1.59: 31750 1.59 - 1.71: 625 1.71 - 1.84: 377 Bond restraints: 75500 Sorted by residual: bond pdb=" C THR a 645 " pdb=" N PRO a 646 " ideal model delta sigma weight residual 1.336 1.389 -0.054 1.23e-02 6.61e+03 1.91e+01 bond pdb=" C ALA N 321 " pdb=" N PRO N 322 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.58e+00 bond pdb=" C LYS C 729 " pdb=" N PRO C 730 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.71e+00 bond pdb=" CA ILE C 754 " pdb=" CB ILE C 754 " ideal model delta sigma weight residual 1.534 1.551 -0.017 6.80e-03 2.16e+04 5.96e+00 bond pdb=" CA ILE C 754 " pdb=" C ILE C 754 " ideal model delta sigma weight residual 1.520 1.541 -0.021 8.80e-03 1.29e+04 5.81e+00 ... (remaining 75495 not shown) Histogram of bond angle deviations from ideal: 95.39 - 103.69: 1815 103.69 - 111.99: 38083 111.99 - 120.30: 32524 120.30 - 128.60: 31496 128.60 - 136.90: 756 Bond angle restraints: 104674 Sorted by residual: angle pdb=" C ASP a 519 " pdb=" N TYR a 520 " pdb=" CA TYR a 520 " ideal model delta sigma weight residual 121.54 136.90 -15.36 1.91e+00 2.74e-01 6.47e+01 angle pdb=" N GLU Q 65 " pdb=" CA GLU Q 65 " pdb=" CB GLU Q 65 " ideal model delta sigma weight residual 110.40 120.15 -9.75 1.63e+00 3.76e-01 3.58e+01 angle pdb=" CB MET Y 207 " pdb=" CG MET Y 207 " pdb=" SD MET Y 207 " ideal model delta sigma weight residual 112.70 130.58 -17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C GLU b 56 " pdb=" N VAL b 57 " pdb=" CA VAL b 57 " ideal model delta sigma weight residual 121.97 132.03 -10.06 1.80e+00 3.09e-01 3.13e+01 angle pdb=" CB MET N 997 " pdb=" CG MET N 997 " pdb=" SD MET N 997 " ideal model delta sigma weight residual 112.70 129.10 -16.40 3.00e+00 1.11e-01 2.99e+01 ... (remaining 104669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 44064 35.84 - 71.68: 1247 71.68 - 107.52: 129 107.52 - 143.36: 3 143.36 - 179.20: 12 Dihedral angle restraints: 45455 sinusoidal: 17097 harmonic: 28358 Sorted by residual: dihedral pdb=" O4' U g 154 " pdb=" C1' U g 154 " pdb=" N1 U g 154 " pdb=" C2 U g 154 " ideal model delta sinusoidal sigma weight residual 200.00 37.94 162.06 1 1.50e+01 4.44e-03 8.33e+01 dihedral pdb=" O4' U g -14 " pdb=" C1' U g -14 " pdb=" N1 U g -14 " pdb=" C2 U g -14 " ideal model delta sinusoidal sigma weight residual 200.00 40.67 159.33 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' C e 23 " pdb=" C1' C e 23 " pdb=" N1 C e 23 " pdb=" C2 C e 23 " ideal model delta sinusoidal sigma weight residual 200.00 74.95 125.05 1 1.50e+01 4.44e-03 6.72e+01 ... (remaining 45452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.997: 12555 0.997 - 1.993: 0 1.993 - 2.990: 0 2.990 - 3.987: 0 3.987 - 4.984: 4 Chirality restraints: 12559 Sorted by residual: chirality pdb=" C2 IHP a3001 " pdb=" C1 IHP a3001 " pdb=" C3 IHP a3001 " pdb=" O12 IHP a3001 " both_signs ideal model delta sigma weight residual False -2.52 2.46 -4.98 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" C5 IHP a3001 " pdb=" C4 IHP a3001 " pdb=" C6 IHP a3001 " pdb=" O15 IHP a3001 " both_signs ideal model delta sigma weight residual False -2.42 2.35 -4.77 2.00e-01 2.50e+01 5.69e+02 chirality pdb=" C3 IHP a3001 " pdb=" C2 IHP a3001 " pdb=" C4 IHP a3001 " pdb=" O13 IHP a3001 " both_signs ideal model delta sigma weight residual False -2.34 2.38 -4.72 2.00e-01 2.50e+01 5.56e+02 ... (remaining 12556 not shown) Planarity restraints: 12556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 579 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL N 579 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL N 579 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP N 580 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL Y 306 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL Y 306 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL Y 306 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU Y 307 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG Y 303 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C ARG Y 303 " 0.067 2.00e-02 2.50e+03 pdb=" O ARG Y 303 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU Y 304 " -0.023 2.00e-02 2.50e+03 ... (remaining 12553 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1743 2.68 - 3.23: 64899 3.23 - 3.79: 122050 3.79 - 4.34: 150849 4.34 - 4.90: 240971 Nonbonded interactions: 580512 Sorted by model distance: nonbonded pdb=" OP1 C d 55 " pdb="MG MG d 205 " model vdw 2.124 2.170 nonbonded pdb=" NE2 HIS I 78 " pdb="ZN ZN I 600 " model vdw 2.126 1.848 nonbonded pdb=" O1G GTP b1500 " pdb="MG MG b1501 " model vdw 2.127 2.170 nonbonded pdb=" OP2 G d 75 " pdb="MG MG d 204 " model vdw 2.140 2.170 nonbonded pdb=" OP2 U d 74 " pdb="MG MG d 201 " model vdw 2.141 2.170 ... (remaining 580507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 7.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.050 Extract box with map and model: 30.520 Check model and map are aligned: 0.830 Set scattering table: 0.510 Process input model: 196.440 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 241.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.004 0.103 75500 Z= 0.297 Angle : 0.848 17.877 104674 Z= 0.453 Chirality : 0.099 4.984 12559 Planarity : 0.007 0.077 12556 Dihedral : 16.590 179.202 27027 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.53 % Favored : 95.23 % Rotamer: Outliers : 0.04 % Allowed : 0.36 % Favored : 99.60 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.72 % 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: -2.31 (0.07), residues: 9607 helix: -1.77 (0.06), residues: 3853 sheet: -0.15 (0.15), residues: 1315 loop : -1.64 (0.09), residues: 4439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 939 HIS 0.015 0.001 HIS J 425 PHE 0.031 0.002 PHE a 387 TYR 0.060 0.002 TYR X 282 ARG 0.010 0.000 ARG N 668 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 252 time to evaluate : 6.209 Fit side-chains revert: symmetry clash REVERT: N 823 MET cc_start: 0.8935 (tpt) cc_final: 0.8667 (tpt) REVERT: N 827 MET cc_start: 0.9516 (mmp) cc_final: 0.9281 (mmp) REVERT: N 997 MET cc_start: 0.8272 (mmm) cc_final: 0.7339 (mmm) REVERT: O 185 MET cc_start: 0.6326 (tmm) cc_final: 0.5949 (tmm) REVERT: a 1327 MET cc_start: 0.8857 (tpp) cc_final: 0.8404 (ttt) outliers start: 2 outliers final: 2 residues processed: 254 average time/residue: 0.6329 time to fit residues: 297.3408 Evaluate side-chains 249 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 6.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 458 THR Chi-restraints excluded: chain W residue 575 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 836 optimal weight: 6.9990 chunk 751 optimal weight: 9.9990 chunk 416 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 506 optimal weight: 8.9990 chunk 401 optimal weight: 1.9990 chunk 776 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 chunk 472 optimal weight: 40.0000 chunk 578 optimal weight: 0.5980 chunk 899 optimal weight: 20.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 431 GLN ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 483 GLN a 960 ASN a1217 GLN a1218 ASN ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 75500 Z= 0.220 Angle : 0.523 22.081 104674 Z= 0.267 Chirality : 0.042 0.925 12559 Planarity : 0.004 0.059 12556 Dihedral : 15.402 178.301 15629 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.65 % Favored : 96.14 % Rotamer: Outliers : 0.18 % Allowed : 3.58 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.66 (0.08), residues: 9607 helix: 0.40 (0.08), residues: 3861 sheet: -0.05 (0.15), residues: 1319 loop : -1.28 (0.09), residues: 4427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 273 HIS 0.005 0.001 HIS J 431 PHE 0.018 0.001 PHE a1099 TYR 0.026 0.001 TYR X 282 ARG 0.003 0.000 ARG N 668 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 246 time to evaluate : 6.277 Fit side-chains revert: symmetry clash REVERT: J 435 MET cc_start: 0.5219 (mtt) cc_final: 0.4462 (ptp) REVERT: N 500 MET cc_start: 0.9106 (mmp) cc_final: 0.8830 (mmp) REVERT: O 185 MET cc_start: 0.6491 (tmm) cc_final: 0.5930 (tmm) REVERT: Y 125 MET cc_start: 0.8453 (ppp) cc_final: 0.7750 (ppp) REVERT: a 503 MET cc_start: 0.8632 (ptp) cc_final: 0.8278 (ptp) REVERT: a 591 MET cc_start: 0.8808 (tpp) cc_final: 0.8506 (ttm) REVERT: a 1652 MET cc_start: 0.8141 (tpp) cc_final: 0.7609 (tpp) REVERT: b 105 MET cc_start: 0.9187 (mmm) cc_final: 0.8739 (mmm) REVERT: b 687 MET cc_start: 0.7966 (tmm) cc_final: 0.7746 (tmm) outliers start: 9 outliers final: 6 residues processed: 251 average time/residue: 0.6343 time to fit residues: 295.6335 Evaluate side-chains 252 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 6.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 654 ASP Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain W residue 458 THR Chi-restraints excluded: chain W residue 557 THR Chi-restraints excluded: chain W residue 575 THR Chi-restraints excluded: chain a residue 61 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 500 optimal weight: 10.0000 chunk 279 optimal weight: 8.9990 chunk 749 optimal weight: 0.1980 chunk 612 optimal weight: 0.9980 chunk 248 optimal weight: 50.0000 chunk 901 optimal weight: 40.0000 chunk 973 optimal weight: 50.0000 chunk 802 optimal weight: 0.9980 chunk 894 optimal weight: 50.0000 chunk 307 optimal weight: 20.0000 chunk 723 optimal weight: 10.0000 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 196 ASN ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 960 ASN ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 75500 Z= 0.239 Angle : 0.494 10.379 104674 Z= 0.256 Chirality : 0.040 0.351 12559 Planarity : 0.003 0.052 12556 Dihedral : 15.287 178.604 15629 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.96 % Favored : 95.84 % Rotamer: Outliers : 0.20 % Allowed : 5.81 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.25 (0.09), residues: 9607 helix: 1.48 (0.08), residues: 3868 sheet: 0.01 (0.15), residues: 1325 loop : -0.97 (0.09), residues: 4414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 231 HIS 0.004 0.001 HIS T 53 PHE 0.018 0.001 PHE a1099 TYR 0.023 0.001 TYR u 241 ARG 0.004 0.000 ARG a1427 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 245 time to evaluate : 6.403 Fit side-chains REVERT: N 500 MET cc_start: 0.9208 (mmp) cc_final: 0.8797 (mmp) REVERT: N 706 MET cc_start: 0.9447 (tmm) cc_final: 0.9068 (tmm) REVERT: O 185 MET cc_start: 0.6711 (tmm) cc_final: 0.6108 (tmm) REVERT: V 96 MET cc_start: 0.9053 (mmm) cc_final: 0.8617 (mmm) REVERT: V 226 MET cc_start: 0.8382 (mmm) cc_final: 0.8097 (mmm) REVERT: Y 125 MET cc_start: 0.8497 (ppp) cc_final: 0.7950 (ppp) REVERT: a 1652 MET cc_start: 0.8340 (tpp) cc_final: 0.7565 (tpp) REVERT: b 123 MET cc_start: 0.8976 (mmm) cc_final: 0.8365 (mmm) REVERT: b 641 MET cc_start: 0.8976 (tpp) cc_final: 0.8767 (mmm) outliers start: 10 outliers final: 3 residues processed: 251 average time/residue: 0.6059 time to fit residues: 282.1688 Evaluate side-chains 248 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 245 time to evaluate : 6.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 654 ASP Chi-restraints excluded: chain W residue 557 THR Chi-restraints excluded: chain a residue 61 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 890 optimal weight: 0.9980 chunk 677 optimal weight: 2.9990 chunk 467 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 chunk 430 optimal weight: 6.9990 chunk 605 optimal weight: 0.2980 chunk 904 optimal weight: 50.0000 chunk 957 optimal weight: 50.0000 chunk 472 optimal weight: 50.0000 chunk 857 optimal weight: 20.0000 chunk 258 optimal weight: 40.0000 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1213 ASN D 55 GLN ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 697 GLN N 720 ASN O 370 ASN ** O 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 960 ASN ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 75500 Z= 0.335 Angle : 0.539 10.412 104674 Z= 0.280 Chirality : 0.041 0.237 12559 Planarity : 0.003 0.052 12556 Dihedral : 15.341 178.846 15627 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.32 % Favored : 95.46 % Rotamer: Outliers : 0.38 % Allowed : 7.97 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.70 (0.09), residues: 9607 helix: 2.02 (0.09), residues: 3850 sheet: -0.07 (0.15), residues: 1331 loop : -0.76 (0.10), residues: 4426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 637 HIS 0.005 0.001 HIS T 53 PHE 0.024 0.001 PHE X 333 TYR 0.019 0.001 TYR u 241 ARG 0.004 0.000 ARG a1427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 244 time to evaluate : 6.713 Fit side-chains revert: symmetry clash REVERT: L 534 MET cc_start: 0.8633 (tpt) cc_final: 0.8214 (tmm) REVERT: N 500 MET cc_start: 0.9053 (mmp) cc_final: 0.8843 (mmp) REVERT: N 706 MET cc_start: 0.9362 (tmm) cc_final: 0.9086 (tmm) REVERT: N 908 MET cc_start: 0.8440 (ppp) cc_final: 0.8212 (ppp) REVERT: O 185 MET cc_start: 0.6932 (tmm) cc_final: 0.6025 (tmm) REVERT: V 96 MET cc_start: 0.9121 (mmm) cc_final: 0.8797 (mmm) REVERT: Y 125 MET cc_start: 0.8444 (ppp) cc_final: 0.7990 (ppp) REVERT: Y 207 MET cc_start: 0.9320 (mmp) cc_final: 0.8653 (mmm) REVERT: a 1652 MET cc_start: 0.8640 (tpp) cc_final: 0.7945 (tpp) REVERT: b 641 MET cc_start: 0.9023 (tpp) cc_final: 0.8748 (mmm) outliers start: 19 outliers final: 8 residues processed: 258 average time/residue: 0.6141 time to fit residues: 293.3476 Evaluate side-chains 252 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 244 time to evaluate : 6.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 654 ASP Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain U residue 81 CYS Chi-restraints excluded: chain W residue 557 THR Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain b residue 62 ASP Chi-restraints excluded: chain q residue 19 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 797 optimal weight: 8.9990 chunk 543 optimal weight: 2.9990 chunk 13 optimal weight: 50.0000 chunk 713 optimal weight: 7.9990 chunk 395 optimal weight: 2.9990 chunk 817 optimal weight: 7.9990 chunk 662 optimal weight: 0.8980 chunk 1 optimal weight: 50.0000 chunk 489 optimal weight: 40.0000 chunk 859 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 206 ASN ** W 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 960 ASN ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 75500 Z= 0.204 Angle : 0.476 10.521 104674 Z= 0.246 Chirality : 0.039 0.252 12559 Planarity : 0.003 0.051 12556 Dihedral : 15.302 179.621 15627 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.99 % Favored : 95.79 % Rotamer: Outliers : 0.38 % Allowed : 9.00 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.93 (0.09), residues: 9607 helix: 2.27 (0.09), residues: 3865 sheet: 0.02 (0.15), residues: 1323 loop : -0.70 (0.10), residues: 4419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 273 HIS 0.004 0.001 HIS T 53 PHE 0.018 0.001 PHE a1099 TYR 0.027 0.001 TYR a 520 ARG 0.003 0.000 ARG a1427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 246 time to evaluate : 6.328 Fit side-chains REVERT: L 534 MET cc_start: 0.8731 (tpt) cc_final: 0.8425 (tmm) REVERT: N 706 MET cc_start: 0.9382 (tmm) cc_final: 0.9056 (tmm) REVERT: N 908 MET cc_start: 0.8340 (ppp) cc_final: 0.8086 (ppp) REVERT: O 185 MET cc_start: 0.6937 (tmm) cc_final: 0.6030 (tmm) REVERT: Q 64 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8564 (pt0) REVERT: V 96 MET cc_start: 0.9119 (mmm) cc_final: 0.8682 (mmm) REVERT: Y 125 MET cc_start: 0.8328 (ppp) cc_final: 0.7935 (ppp) REVERT: Y 207 MET cc_start: 0.9266 (mmp) cc_final: 0.8533 (mmm) REVERT: a 1591 MET cc_start: 0.8790 (mmm) cc_final: 0.8503 (mmm) REVERT: a 1652 MET cc_start: 0.8657 (tpp) cc_final: 0.8330 (tpp) REVERT: b 641 MET cc_start: 0.9007 (tpp) cc_final: 0.8710 (mmm) outliers start: 19 outliers final: 11 residues processed: 257 average time/residue: 0.6257 time to fit residues: 298.9446 Evaluate side-chains 257 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 245 time to evaluate : 6.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 654 ASP Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain a residue 696 MET Chi-restraints excluded: chain a residue 738 MET Chi-restraints excluded: chain b residue 62 ASP Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 481 MET Chi-restraints excluded: chain b residue 603 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 322 optimal weight: 20.0000 chunk 862 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 562 optimal weight: 0.1980 chunk 236 optimal weight: 50.0000 chunk 958 optimal weight: 50.0000 chunk 795 optimal weight: 10.0000 chunk 443 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 317 optimal weight: 40.0000 chunk 503 optimal weight: 9.9990 overall best weight: 7.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 919 ASN ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 960 ASN a1188 ASN ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 75500 Z= 0.421 Angle : 0.582 11.762 104674 Z= 0.300 Chirality : 0.042 0.270 12559 Planarity : 0.004 0.051 12556 Dihedral : 15.398 178.819 15627 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.85 % Favored : 94.93 % Rotamer: Outliers : 0.71 % Allowed : 10.25 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.92 (0.09), residues: 9607 helix: 2.28 (0.09), residues: 3875 sheet: -0.12 (0.15), residues: 1314 loop : -0.69 (0.10), residues: 4418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 637 HIS 0.006 0.001 HIS T 53 PHE 0.020 0.001 PHE X 333 TYR 0.029 0.001 TYR a 520 ARG 0.005 0.000 ARG a1354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 245 time to evaluate : 6.404 Fit side-chains revert: symmetry clash REVERT: N 500 MET cc_start: 0.9131 (mmp) cc_final: 0.8931 (mmp) REVERT: N 706 MET cc_start: 0.9334 (tmm) cc_final: 0.9097 (tmm) REVERT: N 908 MET cc_start: 0.8456 (ppp) cc_final: 0.8173 (ppp) REVERT: O 185 MET cc_start: 0.7460 (tmm) cc_final: 0.6482 (tmm) REVERT: V 96 MET cc_start: 0.9137 (mmm) cc_final: 0.8677 (mmm) REVERT: Y 125 MET cc_start: 0.8320 (ppp) cc_final: 0.7982 (ppp) REVERT: Y 207 MET cc_start: 0.9341 (mmp) cc_final: 0.8441 (mmm) REVERT: Y 412 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8537 (t80) REVERT: a 1652 MET cc_start: 0.8722 (tpp) cc_final: 0.8405 (tpp) REVERT: b 105 MET cc_start: 0.9151 (mmm) cc_final: 0.8940 (mmm) REVERT: b 641 MET cc_start: 0.9098 (tpp) cc_final: 0.8753 (mmm) outliers start: 36 outliers final: 16 residues processed: 274 average time/residue: 0.6144 time to fit residues: 310.8000 Evaluate side-chains 261 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 6.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain O residue 304 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain U residue 81 CYS Chi-restraints excluded: chain W residue 557 THR Chi-restraints excluded: chain W residue 575 THR Chi-restraints excluded: chain Y residue 412 PHE Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 330 THR Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain a residue 1121 ASN Chi-restraints excluded: chain b residue 62 ASP Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 603 MET Chi-restraints excluded: chain q residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 924 optimal weight: 40.0000 chunk 108 optimal weight: 20.0000 chunk 546 optimal weight: 3.9990 chunk 700 optimal weight: 0.9990 chunk 542 optimal weight: 9.9990 chunk 807 optimal weight: 10.0000 chunk 535 optimal weight: 9.9990 chunk 955 optimal weight: 20.0000 chunk 597 optimal weight: 1.9990 chunk 582 optimal weight: 3.9990 chunk 440 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 960 ASN ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 75500 Z= 0.169 Angle : 0.479 12.023 104674 Z= 0.246 Chirality : 0.039 0.264 12559 Planarity : 0.003 0.052 12556 Dihedral : 15.329 179.971 15627 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.76 % Favored : 96.03 % Rotamer: Outliers : 0.51 % Allowed : 10.98 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 1.09 (0.09), residues: 9607 helix: 2.45 (0.09), residues: 3878 sheet: 0.01 (0.15), residues: 1310 loop : -0.63 (0.10), residues: 4419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 273 HIS 0.004 0.001 HIS a1209 PHE 0.017 0.001 PHE a1099 TYR 0.026 0.001 TYR a 520 ARG 0.003 0.000 ARG N 668 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 6.451 Fit side-chains revert: symmetry clash REVERT: N 500 MET cc_start: 0.9176 (mmp) cc_final: 0.8801 (mmp) REVERT: N 706 MET cc_start: 0.9374 (tmm) cc_final: 0.9066 (tmm) REVERT: N 908 MET cc_start: 0.8438 (ppp) cc_final: 0.8167 (ppp) REVERT: O 185 MET cc_start: 0.7096 (tmm) cc_final: 0.6108 (tmm) REVERT: Q 64 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8498 (mt-10) REVERT: V 96 MET cc_start: 0.9088 (mmm) cc_final: 0.8624 (mmm) REVERT: Y 125 MET cc_start: 0.8228 (ppp) cc_final: 0.7942 (ppp) REVERT: Y 207 MET cc_start: 0.9319 (mmp) cc_final: 0.8645 (mmm) REVERT: Y 412 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8418 (t80) REVERT: a 1652 MET cc_start: 0.8685 (tpp) cc_final: 0.8341 (tpp) REVERT: b 641 MET cc_start: 0.9026 (tpp) cc_final: 0.8698 (mmm) outliers start: 26 outliers final: 11 residues processed: 266 average time/residue: 0.6046 time to fit residues: 297.3992 Evaluate side-chains 258 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 245 time to evaluate : 6.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain U residue 81 CYS Chi-restraints excluded: chain W residue 557 THR Chi-restraints excluded: chain Y residue 412 PHE Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain b residue 62 ASP Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 747 ASP Chi-restraints excluded: chain q residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 590 optimal weight: 8.9990 chunk 381 optimal weight: 10.0000 chunk 570 optimal weight: 30.0000 chunk 287 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 607 optimal weight: 0.9990 chunk 650 optimal weight: 3.9990 chunk 472 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 750 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 960 ASN ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 75500 Z= 0.342 Angle : 0.542 13.197 104674 Z= 0.278 Chirality : 0.041 0.258 12559 Planarity : 0.003 0.050 12556 Dihedral : 15.352 179.009 15627 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.67 % Favored : 95.12 % Rotamer: Outliers : 0.49 % Allowed : 11.19 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.09 (0.09), residues: 9607 helix: 2.46 (0.09), residues: 3872 sheet: -0.05 (0.15), residues: 1298 loop : -0.61 (0.10), residues: 4437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 637 HIS 0.006 0.001 HIS T 53 PHE 0.019 0.001 PHE a1207 TYR 0.026 0.001 TYR a 520 ARG 0.004 0.000 ARG a1354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 245 time to evaluate : 8.352 Fit side-chains revert: symmetry clash REVERT: C 1006 MET cc_start: 0.8791 (mpp) cc_final: 0.8338 (mmt) REVERT: N 500 MET cc_start: 0.9199 (mmp) cc_final: 0.8848 (mmp) REVERT: N 706 MET cc_start: 0.9334 (tmm) cc_final: 0.9078 (tmm) REVERT: O 185 MET cc_start: 0.7326 (tmm) cc_final: 0.6323 (tmm) REVERT: Q 64 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: V 96 MET cc_start: 0.9105 (mmm) cc_final: 0.8639 (mmm) REVERT: Y 207 MET cc_start: 0.9319 (mmp) cc_final: 0.8585 (mmm) REVERT: Y 412 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8483 (t80) REVERT: b 641 MET cc_start: 0.9070 (tpp) cc_final: 0.8710 (mmm) outliers start: 25 outliers final: 16 residues processed: 265 average time/residue: 0.6224 time to fit residues: 304.4338 Evaluate side-chains 262 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 244 time to evaluate : 6.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain N residue 604 VAL Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain U residue 81 CYS Chi-restraints excluded: chain W residue 557 THR Chi-restraints excluded: chain W residue 575 THR Chi-restraints excluded: chain Y residue 412 PHE Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain b residue 62 ASP Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 481 MET Chi-restraints excluded: chain b residue 603 MET Chi-restraints excluded: chain b residue 747 ASP Chi-restraints excluded: chain q residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 868 optimal weight: 8.9990 chunk 915 optimal weight: 0.0770 chunk 834 optimal weight: 8.9990 chunk 890 optimal weight: 2.9990 chunk 914 optimal weight: 7.9990 chunk 535 optimal weight: 30.0000 chunk 387 optimal weight: 9.9990 chunk 698 optimal weight: 0.9990 chunk 273 optimal weight: 9.9990 chunk 804 optimal weight: 0.7980 chunk 841 optimal weight: 10.0000 overall best weight: 2.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 960 ASN ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 75500 Z= 0.171 Angle : 0.482 13.496 104674 Z= 0.246 Chirality : 0.039 0.257 12559 Planarity : 0.003 0.050 12556 Dihedral : 15.303 179.796 15627 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.03 % Favored : 95.76 % Rotamer: Outliers : 0.38 % Allowed : 11.37 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.09), residues: 9607 helix: 2.54 (0.09), residues: 3867 sheet: 0.05 (0.15), residues: 1311 loop : -0.59 (0.10), residues: 4429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 273 HIS 0.003 0.001 HIS Y 231 PHE 0.017 0.001 PHE a1207 TYR 0.024 0.001 TYR a 520 ARG 0.003 0.000 ARG a1427 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 245 time to evaluate : 7.906 Fit side-chains REVERT: C 1006 MET cc_start: 0.8764 (mpp) cc_final: 0.8302 (mmt) REVERT: J 435 MET cc_start: 0.6164 (mtt) cc_final: 0.5773 (mtm) REVERT: N 500 MET cc_start: 0.9221 (mmp) cc_final: 0.8895 (mmp) REVERT: N 706 MET cc_start: 0.9364 (tmm) cc_final: 0.8916 (tmm) REVERT: N 846 MET cc_start: 0.9377 (mmt) cc_final: 0.9119 (mmt) REVERT: O 185 MET cc_start: 0.7289 (tmm) cc_final: 0.6347 (tmm) REVERT: Q 64 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8495 (mt-10) REVERT: V 96 MET cc_start: 0.9082 (mmm) cc_final: 0.8631 (mmm) REVERT: Y 207 MET cc_start: 0.9266 (mmp) cc_final: 0.8540 (mmm) REVERT: Y 412 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8430 (t80) REVERT: a 1271 MET cc_start: 0.8861 (mmm) cc_final: 0.8546 (mmm) REVERT: a 1652 MET cc_start: 0.8714 (tpp) cc_final: 0.8360 (tpp) REVERT: b 105 MET cc_start: 0.8922 (mmm) cc_final: 0.8438 (mmm) REVERT: b 641 MET cc_start: 0.9028 (tpp) cc_final: 0.8691 (mmm) outliers start: 19 outliers final: 15 residues processed: 261 average time/residue: 0.6017 time to fit residues: 293.3426 Evaluate side-chains 262 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 245 time to evaluate : 6.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain U residue 81 CYS Chi-restraints excluded: chain W residue 575 THR Chi-restraints excluded: chain Y residue 412 PHE Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 220 VAL Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain a residue 1121 ASN Chi-restraints excluded: chain a residue 1429 THR Chi-restraints excluded: chain b residue 62 ASP Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 603 MET Chi-restraints excluded: chain q residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 886 optimal weight: 40.0000 chunk 584 optimal weight: 6.9990 chunk 941 optimal weight: 6.9990 chunk 574 optimal weight: 0.9980 chunk 446 optimal weight: 0.0770 chunk 654 optimal weight: 8.9990 chunk 987 optimal weight: 0.0040 chunk 908 optimal weight: 40.0000 chunk 786 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 607 optimal weight: 9.9990 overall best weight: 3.0154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 GLN ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 231 HIS ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 75500 Z= 0.189 Angle : 0.482 13.829 104674 Z= 0.246 Chirality : 0.039 0.244 12559 Planarity : 0.003 0.049 12556 Dihedral : 15.256 179.310 15627 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer: Outliers : 0.45 % Allowed : 11.33 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.09), residues: 9607 helix: 2.58 (0.09), residues: 3870 sheet: 0.07 (0.15), residues: 1312 loop : -0.57 (0.10), residues: 4425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 750 HIS 0.004 0.001 HIS T 53 PHE 0.016 0.001 PHE a1207 TYR 0.022 0.001 TYR a 520 ARG 0.003 0.000 ARG N 668 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19214 Ramachandran restraints generated. 9607 Oldfield, 0 Emsley, 9607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 6.355 Fit side-chains revert: symmetry clash REVERT: C 1006 MET cc_start: 0.8753 (mpp) cc_final: 0.8309 (mmt) REVERT: J 435 MET cc_start: 0.6145 (mtt) cc_final: 0.5772 (mtm) REVERT: L 534 MET cc_start: 0.8401 (tpt) cc_final: 0.7984 (tmm) REVERT: N 500 MET cc_start: 0.9219 (mmp) cc_final: 0.8881 (mmp) REVERT: N 706 MET cc_start: 0.9365 (tmm) cc_final: 0.8992 (tmm) REVERT: N 846 MET cc_start: 0.9364 (mmt) cc_final: 0.9093 (mmt) REVERT: Q 64 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8498 (mt-10) REVERT: V 96 MET cc_start: 0.9066 (mmm) cc_final: 0.8618 (mmm) REVERT: Y 207 MET cc_start: 0.9301 (mmp) cc_final: 0.8548 (mmm) REVERT: Y 412 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8467 (t80) REVERT: a 1591 MET cc_start: 0.8787 (mmm) cc_final: 0.8533 (mmm) REVERT: a 1652 MET cc_start: 0.8761 (tpp) cc_final: 0.8270 (tpp) REVERT: b 105 MET cc_start: 0.8949 (mmm) cc_final: 0.8296 (mmm) REVERT: b 641 MET cc_start: 0.9027 (tpp) cc_final: 0.8687 (mmm) outliers start: 23 outliers final: 17 residues processed: 264 average time/residue: 0.6219 time to fit residues: 303.6518 Evaluate side-chains 264 residues out of total 8630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 245 time to evaluate : 6.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain N residue 818 LEU Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain T residue 105 CYS Chi-restraints excluded: chain U residue 81 CYS Chi-restraints excluded: chain W residue 575 THR Chi-restraints excluded: chain Y residue 412 PHE Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 220 VAL Chi-restraints excluded: chain a residue 520 TYR Chi-restraints excluded: chain a residue 1121 ASN Chi-restraints excluded: chain a residue 1429 THR Chi-restraints excluded: chain b residue 62 ASP Chi-restraints excluded: chain b residue 255 VAL Chi-restraints excluded: chain b residue 481 MET Chi-restraints excluded: chain b residue 603 MET Chi-restraints excluded: chain b residue 747 ASP Chi-restraints excluded: chain q residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 991 random chunks: chunk 482 optimal weight: 6.9990 chunk 624 optimal weight: 0.9980 chunk 837 optimal weight: 3.9990 chunk 240 optimal weight: 40.0000 chunk 724 optimal weight: 2.9990 chunk 116 optimal weight: 50.0000 chunk 218 optimal weight: 8.9990 chunk 787 optimal weight: 0.0470 chunk 329 optimal weight: 6.9990 chunk 808 optimal weight: 3.9990 chunk 99 optimal weight: 50.0000 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 HIS a 483 GLN ** a1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.042990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.032759 restraints weight = 871017.178| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.60 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 75500 Z= 0.161 Angle : 0.473 14.088 104674 Z= 0.241 Chirality : 0.039 0.240 12559 Planarity : 0.003 0.049 12556 Dihedral : 15.217 179.344 15627 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.95 % Favored : 95.87 % Rotamer: Outliers : 0.36 % Allowed : 11.41 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.09), residues: 9607 helix: 2.59 (0.09), residues: 3877 sheet: 0.11 (0.15), residues: 1327 loop : -0.56 (0.10), residues: 4403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 273 HIS 0.003 0.000 HIS T 53 PHE 0.016 0.001 PHE b 770 TYR 0.021 0.001 TYR a 520 ARG 0.003 0.000 ARG N 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10670.03 seconds wall clock time: 191 minutes 34.45 seconds (11494.45 seconds total)