Starting phenix.real_space_refine on Wed Feb 14 09:14:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycx_33741/02_2024/7ycx_33741_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycx_33741/02_2024/7ycx_33741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycx_33741/02_2024/7ycx_33741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycx_33741/02_2024/7ycx_33741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycx_33741/02_2024/7ycx_33741_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycx_33741/02_2024/7ycx_33741_neut.pdb" } resolution = 4.18 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 10 6.06 5 P 104 5.49 5 Mg 1 5.21 5 S 646 5.16 5 C 71096 2.51 5 N 19845 2.21 5 O 21385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 659": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B GLU 776": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B GLU 952": "OE1" <-> "OE2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B GLU 1044": "OE1" <-> "OE2" Residue "B GLU 1119": "OE1" <-> "OE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 826": "OE1" <-> "OE2" Residue "E GLU 694": "OE1" <-> "OE2" Residue "E GLU 890": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 148": "OD1" <-> "OD2" Residue "G GLU 567": "OE1" <-> "OE2" Residue "G GLU 676": "OE1" <-> "OE2" Residue "G GLU 832": "OE1" <-> "OE2" Residue "G GLU 878": "OE1" <-> "OE2" Residue "G GLU 932": "OE1" <-> "OE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 338": "OE1" <-> "OE2" Residue "I GLU 424": "OE1" <-> "OE2" Residue "I GLU 431": "OE1" <-> "OE2" Residue "K GLU 385": "OE1" <-> "OE2" Residue "K PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 37": "OE1" <-> "OE2" Residue "1 GLU 219": "OE1" <-> "OE2" Residue "1 GLU 392": "OE1" <-> "OE2" Residue "1 GLU 500": "OE1" <-> "OE2" Residue "1 GLU 556": "OE1" <-> "OE2" Residue "1 GLU 818": "OE1" <-> "OE2" Residue "1 GLU 1433": "OE1" <-> "OE2" Residue "1 GLU 1456": "OE1" <-> "OE2" Residue "2 TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 13": "OE1" <-> "OE2" Residue "3 GLU 109": "OE1" <-> "OE2" Residue "7 GLU 19": "OE1" <-> "OE2" Residue "9 GLU 97": "OE1" <-> "OE2" Residue "i GLU 29": "OE1" <-> "OE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 113089 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 13054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1779, 13054 Classifications: {'peptide': 1779} Incomplete info: {'truncation_to_alanine': 317} Link IDs: {'PCIS': 3, 'PTRANS': 84, 'TRANS': 1691} Chain breaks: 11 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1115 Unresolved non-hydrogen angles: 1424 Unresolved non-hydrogen dihedrals: 919 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 15, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 14, 'PHE:plan': 18, 'GLU:plan': 19, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 597 Chain: "B" Number of atoms: 8328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8328 Classifications: {'peptide': 1061} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1008} Chain breaks: 7 Chain: "D" Number of atoms: 6205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6205 Classifications: {'peptide': 828} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 787} Chain breaks: 6 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 473 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 170 Chain: "E" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 5244 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 241} Link IDs: {'PTRANS': 61, 'TRANS': 736} Chain breaks: 1 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 784 Unresolved non-hydrogen angles: 1009 Unresolved non-hydrogen dihedrals: 642 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 15, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 12, 'PHE:plan': 8, 'GLU:plan': 12, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 370 Chain: "F" Number of atoms: 4395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4395 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 511} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 6928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 6928 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 32, 'TRANS': 877} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "H" Number of atoms: 7440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 937, 7440 Classifications: {'peptide': 937} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 894} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "I" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4985 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 4, 'PTRANS': 44, 'TRANS': 584} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4646 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 563} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 4527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4527 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 554} Chain: "Q" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2366 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 281} Chain: "U" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 135 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "1" Number of atoms: 11345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1451, 11345 Classifications: {'peptide': 1451} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 2, 'PTRANS': 73, 'TRANS': 1375} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 12, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "2" Number of atoms: 8649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8649 Classifications: {'peptide': 1113} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 53, 'TRANS': 1059} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 1, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 166 Chain: "3" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2048 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "4" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "5" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "6" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "7" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 950 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "8" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "9" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 937 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "a" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "b" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 752 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "c" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 406 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 19} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {' G%rna3p_pur:plan2': 4, ' C%rna3p_pyr:plan': 2, ' A%rna3p_pur:plan2': 3, ' C%rna3p_pyr:plan2': 2, ' G%rna3p_pur:plan': 4, ' A%rna3p_pur:plan': 3} Unresolved non-hydrogen planarities: 108 Chain: "d" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 909 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "e" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1410 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain: "f" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 1920 Classifications: {'peptide': 480} Incomplete info: {'backbone_only': 456} Link IDs: {'PTRANS': 18, 'TRANS': 461} Chain breaks: 6 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 2001 Unresolved non-hydrogen angles: 2880 Unresolved non-hydrogen dihedrals: 1268 Unresolved non-hydrogen chiralities: 612 Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 25, 'TYR:plan': 9, 'ASN:plan1': 11, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 27, 'GLU:plan': 41, 'ASP:plan': 26} Unresolved non-hydrogen planarities: 902 Chain: "g" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 3764 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 510} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 650 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 295 Chain: "h" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 109 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 19} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "i" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "j" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3854 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 16, 'TRANS': 465} Chain breaks: 5 Chain: "k" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1299 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "l" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 997 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69106 SG CYS 1 111 185.223 147.641 202.861 1.00128.27 S ATOM 69134 SG CYS 1 114 185.757 144.334 204.349 1.00122.15 S ATOM 69447 SG CYS 1 154 183.809 147.066 206.254 1.00131.58 S ATOM 69480 SG CYS 1 184 187.084 147.873 206.199 1.00122.48 S ATOM 68802 SG CYS 1 71 179.630 136.362 156.492 1.00120.28 S ATOM 68824 SG CYS 1 74 176.682 133.952 156.651 1.00101.65 S ATOM 68871 SG CYS 1 81 176.005 137.698 156.219 1.00105.96 S ATOM 87928 SG CYS 21119 172.428 127.985 171.496 1.00103.96 S ATOM 87950 SG CYS 21122 174.166 130.437 173.611 1.00107.44 S ATOM 88053 SG CYS 21137 175.701 129.049 170.215 1.00112.14 S ATOM 88074 SG CYS 21140 175.607 127.086 173.565 1.00120.29 S ATOM 89026 SG CYS 3 88 136.969 157.296 104.894 1.00 50.00 S ATOM 89039 SG CYS 3 90 140.623 157.242 104.564 1.00 54.06 S ATOM 89074 SG CYS 3 94 138.754 159.570 102.300 1.00 39.03 S ATOM 89096 SG CYS 3 97 138.822 160.502 105.863 1.00 36.97 S ATOM 94005 SG CYS 7 17 177.907 213.805 211.451 1.00141.22 S ATOM 94029 SG CYS 7 20 179.875 212.391 208.885 1.00155.49 S ATOM 94190 SG CYS 7 39 178.201 209.967 211.356 1.00136.94 S ATOM 94215 SG CYS 7 42 181.186 212.216 212.473 1.00143.16 S ATOM 94567 SG CYS 7 86 141.745 226.709 188.875 1.00112.57 S ATOM 94591 SG CYS 7 89 142.057 229.613 187.030 1.00131.11 S ATOM 94795 SG CYS 7 114 142.155 226.161 185.140 1.00106.92 S ATOM 94830 SG CYS 7 119 145.170 227.202 186.703 1.00118.96 S ATOM 94941 SG CYS 8 7 130.523 182.902 126.963 1.00 49.87 S ATOM 94965 SG CYS 8 10 126.618 182.530 126.220 1.00 43.30 S ATOM 95229 SG CYS 8 44 127.143 184.170 128.924 1.00 39.13 S ATOM 95235 SG CYS 8 45 128.448 185.685 125.586 1.00 37.80 S ATOM 96414 SG CYS a 19 175.771 183.811 120.646 1.00 63.56 S ATOM 96433 SG CYS a 22 176.624 186.792 118.102 1.00 75.27 S ATOM 96550 SG CYS a 36 178.599 183.335 118.125 1.00 83.25 S ATOM 96576 SG CYS a 39 178.785 186.047 120.630 1.00 81.46 S Time building chain proxies: 41.72, per 1000 atoms: 0.37 Number of scatterers: 113089 At special positions: 0 Unit cell: (257.176, 295.12, 260.338, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 10 29.99 Mn 2 24.99 S 646 16.00 P 104 15.00 Mg 1 11.99 O 21385 8.00 N 19845 7.00 C 71096 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: 33.23 Conformation dependent library (CDL) restraints added in 15.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 12102 " pdb="ZN ZN 12102 " - pdb=" SG CYS 1 111 " pdb="ZN ZN 12102 " - pdb=" SG CYS 1 114 " pdb="ZN ZN 12102 " - pdb=" SG CYS 1 154 " pdb="ZN ZN 12102 " - pdb=" SG CYS 1 184 " pdb=" ZN 12103 " pdb="ZN ZN 12103 " - pdb=" NE2 HIS 1 84 " pdb="ZN ZN 12103 " - pdb=" SG CYS 1 74 " pdb="ZN ZN 12103 " - pdb=" SG CYS 1 71 " pdb="ZN ZN 12103 " - pdb=" SG CYS 1 81 " pdb=" ZN 22000 " pdb="ZN ZN 22000 " - pdb=" SG CYS 21119 " pdb="ZN ZN 22000 " - pdb=" SG CYS 21122 " pdb="ZN ZN 22000 " - pdb=" SG CYS 21140 " pdb="ZN ZN 22000 " - pdb=" SG CYS 21137 " pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 94 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 97 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 90 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 88 " pdb=" ZN 7 200 " pdb="ZN ZN 7 200 " - pdb=" SG CYS 7 17 " pdb="ZN ZN 7 200 " - pdb=" SG CYS 7 20 " pdb="ZN ZN 7 200 " - pdb=" SG CYS 7 42 " pdb="ZN ZN 7 200 " - pdb=" SG CYS 7 39 " pdb=" ZN 7 201 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 114 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 89 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 86 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 119 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 10 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 45 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 44 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 7 " pdb=" ZN K 701 " pdb="ZN ZN K 701 " - pdb=" NE2 HIS K 414 " pdb="ZN ZN K 701 " - pdb=" NE2 HIS K 73 " pdb="ZN ZN K 701 " - pdb="ZN ZN K 702 " pdb=" ZN K 702 " pdb="ZN ZN K 702 " - pdb=" NE2 HIS K 157 " pdb="ZN ZN K 702 " - pdb=" NE2 HIS K 68 " pdb="ZN ZN K 702 " - pdb=" ND1 HIS K 70 " pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 39 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 36 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 19 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 22 " Number of angles added : 45 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 27086 Finding SS restraints... Secondary structure from input PDB file: 697 helices and 81 sheets defined 59.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.31 Creating SS restraints... Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 134 through 152 Processing helix chain 'A' and resid 157 through 171 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 223 through 236 removed outlier: 4.129A pdb=" N VAL A 227 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 321 through 339 removed outlier: 3.614A pdb=" N MET A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 360 through 377 removed outlier: 3.888A pdb=" N LYS A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 399 through 412 Processing helix chain 'A' and resid 416 through 434 removed outlier: 3.713A pdb=" N HIS A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 451 removed outlier: 4.396A pdb=" N GLY A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 471 through 487 Processing helix chain 'A' and resid 491 through 507 Processing helix chain 'A' and resid 511 through 521 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 533 through 552 Processing helix chain 'A' and resid 554 through 566 Processing helix chain 'A' and resid 571 through 601 removed outlier: 3.769A pdb=" N LEU A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Proline residue: A 598 - end of helix Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 620 through 626 removed outlier: 4.191A pdb=" N TYR A 624 " --> pdb=" O GLN A 620 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR A 625 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 removed outlier: 4.348A pdb=" N ASN A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 668 through 685 Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.870A pdb=" N ASP A 703 " --> pdb=" O THR A 699 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 709 " --> pdb=" O VAL A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 748 removed outlier: 3.909A pdb=" N TRP A 738 " --> pdb=" O TYR A 734 " (cutoff:3.500A) Proline residue: A 739 - end of helix Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 760 through 773 removed outlier: 3.744A pdb=" N GLU A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 817 Processing helix chain 'A' and resid 828 through 831 removed outlier: 3.745A pdb=" N SER A 831 " --> pdb=" O LEU A 828 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 828 through 831' Processing helix chain 'A' and resid 846 through 861 Processing helix chain 'A' and resid 861 through 869 removed outlier: 3.515A pdb=" N LEU A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 880 removed outlier: 3.744A pdb=" N HIS A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 removed outlier: 4.130A pdb=" N ASP A 893 " --> pdb=" O PRO A 889 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 894 " --> pdb=" O TRP A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 918 Processing helix chain 'A' and resid 939 through 959 Processing helix chain 'A' and resid 964 through 980 removed outlier: 3.628A pdb=" N PHE A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 998 removed outlier: 3.560A pdb=" N ARG A 987 " --> pdb=" O GLN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1025 No H-bonds generated for 'chain 'A' and resid 1023 through 1025' Processing helix chain 'A' and resid 1026 through 1031 Processing helix chain 'A' and resid 1032 through 1036 Processing helix chain 'A' and resid 1038 through 1055 removed outlier: 4.438A pdb=" N SER A1044 " --> pdb=" O ASP A1040 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1074 Processing helix chain 'A' and resid 1078 through 1096 Processing helix chain 'A' and resid 1096 through 1104 Processing helix chain 'A' and resid 1110 through 1133 Processing helix chain 'A' and resid 1163 through 1176 Processing helix chain 'A' and resid 1183 through 1194 Processing helix chain 'A' and resid 1216 through 1226 Processing helix chain 'A' and resid 1228 through 1237 Processing helix chain 'A' and resid 1240 through 1250 Processing helix chain 'A' and resid 1254 through 1272 Processing helix chain 'A' and resid 1272 through 1280 removed outlier: 3.664A pdb=" N LEU A1276 " --> pdb=" O ASP A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1296 removed outlier: 3.574A pdb=" N GLU A1295 " --> pdb=" O GLU A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1310 Processing helix chain 'A' and resid 1389 through 1392 Processing helix chain 'A' and resid 1393 through 1403 Proline residue: A1399 - end of helix Processing helix chain 'A' and resid 1406 through 1424 Proline residue: A1416 - end of helix Processing helix chain 'A' and resid 1431 through 1445 Processing helix chain 'A' and resid 1445 through 1456 Processing helix chain 'A' and resid 1457 through 1475 removed outlier: 3.918A pdb=" N LEU A1461 " --> pdb=" O LEU A1457 " (cutoff:3.500A) Proline residue: A1470 - end of helix Processing helix chain 'A' and resid 1479 through 1500 removed outlier: 4.075A pdb=" N MET A1483 " --> pdb=" O ALA A1479 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU A1484 " --> pdb=" O GLN A1480 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG A1498 " --> pdb=" O LEU A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1519 Processing helix chain 'A' and resid 1527 through 1540 removed outlier: 4.290A pdb=" N GLY A1531 " --> pdb=" O THR A1527 " (cutoff:3.500A) Proline residue: A1538 - end of helix Processing helix chain 'A' and resid 1541 through 1558 Proline residue: A1554 - end of helix Processing helix chain 'A' and resid 1566 through 1572 removed outlier: 4.274A pdb=" N ALA A1570 " --> pdb=" O ALA A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1578 Processing helix chain 'A' and resid 1582 through 1592 Processing helix chain 'A' and resid 1597 through 1609 Processing helix chain 'A' and resid 1614 through 1626 Processing helix chain 'A' and resid 1633 through 1642 Processing helix chain 'A' and resid 1656 through 1667 removed outlier: 3.661A pdb=" N LEU A1660 " --> pdb=" O PHE A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1682 Processing helix chain 'A' and resid 1690 through 1704 removed outlier: 3.725A pdb=" N ILE A1702 " --> pdb=" O LEU A1698 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS A1703 " --> pdb=" O TRP A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1728 through 1744 Processing helix chain 'A' and resid 1750 through 1770 Proline residue: A1763 - end of helix removed outlier: 3.559A pdb=" N CYS A1769 " --> pdb=" O LEU A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1771 through 1780 Processing helix chain 'A' and resid 1790 through 1797 removed outlier: 4.109A pdb=" N VAL A1794 " --> pdb=" O TRP A1790 " (cutoff:3.500A) Processing helix chain 'A' and resid 1797 through 1802 Processing helix chain 'A' and resid 1805 through 1815 removed outlier: 4.048A pdb=" N GLN A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Proline residue: A1811 - end of helix Processing helix chain 'A' and resid 1825 through 1843 removed outlier: 3.544A pdb=" N SER A1830 " --> pdb=" O GLY A1826 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A1843 " --> pdb=" O ILE A1839 " (cutoff:3.500A) Processing helix chain 'A' and resid 1858 through 1873 removed outlier: 4.268A pdb=" N ALA A1862 " --> pdb=" O ARG A1858 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A1863 " --> pdb=" O GLY A1859 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N CYS A1866 " --> pdb=" O ALA A1862 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG A1867 " --> pdb=" O SER A1863 " (cutoff:3.500A) Processing helix chain 'A' and resid 1873 through 1887 removed outlier: 4.244A pdb=" N LEU A1877 " --> pdb=" O HIS A1873 " (cutoff:3.500A) Proline residue: A1882 - end of helix Processing helix chain 'A' and resid 1905 through 1918 Processing helix chain 'A' and resid 1918 through 1924 Processing helix chain 'A' and resid 1928 through 1946 removed outlier: 4.006A pdb=" N TRP A1932 " --> pdb=" O GLN A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1969 Processing helix chain 'A' and resid 1969 through 1981 removed outlier: 3.546A pdb=" N ALA A1973 " --> pdb=" O TYR A1969 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A1978 " --> pdb=" O ALA A1974 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN A1979 " --> pdb=" O ILE A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1981 through 1988 removed outlier: 4.100A pdb=" N LEU A1985 " --> pdb=" O HIS A1981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 1997 removed outlier: 4.288A pdb=" N LEU A1995 " --> pdb=" O ASP A1991 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET A1997 " --> pdb=" O SER A1993 " (cutoff:3.500A) Processing helix chain 'A' and resid 2044 through 2056 Proline residue: A2049 - end of helix removed outlier: 3.594A pdb=" N LYS A2052 " --> pdb=" O ALA A2048 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2075 Processing helix chain 'A' and resid 2077 through 2083 Processing helix chain 'A' and resid 2084 through 2093 removed outlier: 3.572A pdb=" N ARG A2090 " --> pdb=" O THR A2086 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A2091 " --> pdb=" O ASN A2087 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A2093 " --> pdb=" O GLN A2089 " (cutoff:3.500A) Processing helix chain 'A' and resid 2096 through 2114 Processing helix chain 'A' and resid 2117 through 2131 removed outlier: 3.653A pdb=" N PHE A2121 " --> pdb=" O ILE A2117 " (cutoff:3.500A) Proline residue: A2123 - end of helix Processing helix chain 'A' and resid 2135 through 2143 Processing helix chain 'A' and resid 2143 through 2152 removed outlier: 3.727A pdb=" N TYR A2147 " --> pdb=" O ASN A2143 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2169 Processing helix chain 'A' and resid 2173 through 2185 Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 30 through 37 Processing helix chain 'B' and resid 38 through 55 Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 61 through 76 removed outlier: 4.035A pdb=" N SER B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 removed outlier: 4.018A pdb=" N SER B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 193 through 202 Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 220 through 233 removed outlier: 4.652A pdb=" N GLU B 224 " --> pdb=" O ASP B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 257 Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.822A pdb=" N VAL B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 289 removed outlier: 3.543A pdb=" N THR B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 311 through 327 Processing helix chain 'B' and resid 334 through 351 removed outlier: 3.564A pdb=" N ILE B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 398 removed outlier: 4.680A pdb=" N LYS B 384 " --> pdb=" O GLU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 422 through 439 Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'B' and resid 445 through 471 removed outlier: 3.740A pdb=" N LYS B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 462 " --> pdb=" O TRP B 458 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ALA B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 489 removed outlier: 3.600A pdb=" N LEU B 481 " --> pdb=" O GLY B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 504 Processing helix chain 'B' and resid 510 through 524 removed outlier: 3.789A pdb=" N LEU B 514 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 538 removed outlier: 3.674A pdb=" N VAL B 536 " --> pdb=" O THR B 532 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 564 removed outlier: 3.811A pdb=" N CYS B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 569 removed outlier: 3.513A pdb=" N LYS B 568 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 removed outlier: 3.972A pdb=" N ARG B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 620 through 629 removed outlier: 3.574A pdb=" N ASN B 626 " --> pdb=" O GLN B 622 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE B 627 " --> pdb=" O GLU B 623 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 628 " --> pdb=" O ILE B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 665 removed outlier: 3.822A pdb=" N VAL B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 673 removed outlier: 3.680A pdb=" N LEU B 669 " --> pdb=" O ASN B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 688 through 699 Processing helix chain 'B' and resid 705 through 718 Processing helix chain 'B' and resid 719 through 722 Processing helix chain 'B' and resid 723 through 732 removed outlier: 3.530A pdb=" N TRP B 727 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS B 729 " --> pdb=" O ASP B 725 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 731 " --> pdb=" O TRP B 727 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 746 Processing helix chain 'B' and resid 753 through 763 removed outlier: 3.746A pdb=" N ALA B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 780 removed outlier: 4.351A pdb=" N VAL B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU B 780 " --> pdb=" O GLU B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 788 No H-bonds generated for 'chain 'B' and resid 786 through 788' Processing helix chain 'B' and resid 789 through 796 removed outlier: 3.502A pdb=" N ASN B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 806 through 822 removed outlier: 4.136A pdb=" N LEU B 810 " --> pdb=" O PRO B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 837 removed outlier: 3.540A pdb=" N LEU B 828 " --> pdb=" O MET B 824 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 830 " --> pdb=" O ARG B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.503A pdb=" N ILE B 855 " --> pdb=" O ASN B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 861 Processing helix chain 'B' and resid 864 through 869 Processing helix chain 'B' and resid 870 through 900 removed outlier: 3.827A pdb=" N ILE B 876 " --> pdb=" O PRO B 872 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 886 " --> pdb=" O ASN B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 947 Processing helix chain 'B' and resid 949 through 953 Processing helix chain 'B' and resid 990 through 1008 Processing helix chain 'B' and resid 1008 through 1019 removed outlier: 4.257A pdb=" N ALA B1012 " --> pdb=" O ASP B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1032 removed outlier: 4.321A pdb=" N ALA B1030 " --> pdb=" O PRO B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1036 removed outlier: 4.262A pdb=" N HIS B1036 " --> pdb=" O PRO B1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1033 through 1036' Processing helix chain 'B' and resid 1037 through 1047 removed outlier: 4.264A pdb=" N PHE B1041 " --> pdb=" O ILE B1037 " (cutoff:3.500A) Proline residue: B1043 - end of helix removed outlier: 3.806A pdb=" N ALA B1047 " --> pdb=" O PRO B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1068 removed outlier: 3.574A pdb=" N HIS B1063 " --> pdb=" O GLN B1059 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1090 removed outlier: 3.965A pdb=" N LEU B1079 " --> pdb=" O SER B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1101 removed outlier: 3.930A pdb=" N ALA B1098 " --> pdb=" O ALA B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1114 removed outlier: 4.339A pdb=" N SER B1109 " --> pdb=" O PRO B1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1138 removed outlier: 3.617A pdb=" N ALA B1137 " --> pdb=" O ALA B1133 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B1138 " --> pdb=" O SER B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1150 removed outlier: 3.556A pdb=" N ILE B1147 " --> pdb=" O ASP B1144 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B1150 " --> pdb=" O ILE B1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1202 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 50 through 62 Processing helix chain 'D' and resid 68 through 82 removed outlier: 4.446A pdb=" N VAL D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 101 removed outlier: 4.175A pdb=" N ARG D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.709A pdb=" N GLN D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 141 removed outlier: 4.105A pdb=" N LEU D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 159 removed outlier: 3.502A pdb=" N ASP D 153 " --> pdb=" O MET D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 197 through 204 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.658A pdb=" N ARG D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.960A pdb=" N ASN D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS D 239 " --> pdb=" O ASN D 235 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 240 " --> pdb=" O GLN D 236 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER D 242 " --> pdb=" O CYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 263 removed outlier: 4.358A pdb=" N GLN D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR D 263 " --> pdb=" O VAL D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 296 through 309 removed outlier: 3.839A pdb=" N VAL D 300 " --> pdb=" O TRP D 296 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 322 removed outlier: 3.965A pdb=" N GLN D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 378 through 383 Processing helix chain 'D' and resid 387 through 405 removed outlier: 3.922A pdb=" N ARG D 391 " --> pdb=" O MET D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 419 removed outlier: 3.585A pdb=" N CYS D 412 " --> pdb=" O PHE D 408 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASP D 414 " --> pdb=" O GLU D 410 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE D 415 " --> pdb=" O LYS D 411 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 Processing helix chain 'D' and resid 447 through 454 removed outlier: 3.811A pdb=" N ALA D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 474 removed outlier: 3.541A pdb=" N CYS D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 496 Processing helix chain 'D' and resid 499 through 514 removed outlier: 4.125A pdb=" N LYS D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N HIS D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 520 Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 521 through 526 removed outlier: 3.687A pdb=" N LEU D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 555 removed outlier: 3.645A pdb=" N LEU D 550 " --> pdb=" O ALA D 546 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 580 Processing helix chain 'D' and resid 609 through 624 Processing helix chain 'D' and resid 628 through 650 Processing helix chain 'D' and resid 653 through 675 removed outlier: 3.552A pdb=" N ASP D 658 " --> pdb=" O ALA D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 681 removed outlier: 3.680A pdb=" N TRP D 679 " --> pdb=" O GLU D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 711 removed outlier: 3.860A pdb=" N LYS D 698 " --> pdb=" O SER D 694 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR D 711 " --> pdb=" O MET D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 741 Processing helix chain 'D' and resid 743 through 765 Processing helix chain 'D' and resid 775 through 783 Processing helix chain 'D' and resid 783 through 790 removed outlier: 3.663A pdb=" N LEU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 805 removed outlier: 4.030A pdb=" N LYS D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 861 removed outlier: 3.513A pdb=" N THR D 860 " --> pdb=" O ASP D 856 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 209 through 224 Proline residue: E 221 - end of helix Processing helix chain 'E' and resid 225 through 239 Proline residue: E 235 - end of helix removed outlier: 4.018A pdb=" N ILE E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 263 removed outlier: 4.366A pdb=" N SER E 263 " --> pdb=" O GLY E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 274 Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 283 through 288 Processing helix chain 'E' and resid 289 through 292 removed outlier: 3.586A pdb=" N ALA E 292 " --> pdb=" O PRO E 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 289 through 292' Processing helix chain 'E' and resid 293 through 315 Processing helix chain 'E' and resid 316 through 331 Processing helix chain 'E' and resid 337 through 351 Proline residue: E 349 - end of helix Processing helix chain 'E' and resid 353 through 370 removed outlier: 4.476A pdb=" N GLY E 357 " --> pdb=" O GLY E 353 " (cutoff:3.500A) Proline residue: E 365 - end of helix removed outlier: 3.632A pdb=" N VAL E 368 " --> pdb=" O LYS E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 379 Processing helix chain 'E' and resid 383 through 395 removed outlier: 4.133A pdb=" N MET E 387 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 413 Processing helix chain 'E' and resid 418 through 431 removed outlier: 3.887A pdb=" N THR E 422 " --> pdb=" O SER E 418 " (cutoff:3.500A) Proline residue: E 428 - end of helix Processing helix chain 'E' and resid 437 through 461 Proline residue: E 457 - end of helix Processing helix chain 'E' and resid 471 through 479 removed outlier: 4.203A pdb=" N ASN E 479 " --> pdb=" O ASP E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 490 Processing helix chain 'E' and resid 494 through 510 Processing helix chain 'E' and resid 514 through 525 Processing helix chain 'E' and resid 528 through 544 removed outlier: 4.052A pdb=" N VAL E 544 " --> pdb=" O ALA E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 563 removed outlier: 3.905A pdb=" N LEU E 552 " --> pdb=" O GLY E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 587 Processing helix chain 'E' and resid 590 through 595 Processing helix chain 'E' and resid 598 through 605 removed outlier: 3.796A pdb=" N ALA E 605 " --> pdb=" O GLU E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 611 removed outlier: 3.642A pdb=" N ALA E 611 " --> pdb=" O LEU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 616 Processing helix chain 'E' and resid 618 through 632 removed outlier: 3.917A pdb=" N ILE E 631 " --> pdb=" O SER E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 662 Processing helix chain 'E' and resid 663 through 666 Processing helix chain 'E' and resid 667 through 679 removed outlier: 3.585A pdb=" N GLN E 679 " --> pdb=" O THR E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 698 Processing helix chain 'E' and resid 732 through 738 Processing helix chain 'E' and resid 771 through 788 Processing helix chain 'E' and resid 805 through 821 Processing helix chain 'E' and resid 833 through 839 Processing helix chain 'E' and resid 840 through 854 Processing helix chain 'E' and resid 855 through 867 removed outlier: 3.974A pdb=" N GLU E 859 " --> pdb=" O PRO E 855 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA E 867 " --> pdb=" O LEU E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 869 through 874 removed outlier: 3.966A pdb=" N TYR E 873 " --> pdb=" O PRO E 869 " (cutoff:3.500A) Processing helix chain 'E' and resid 874 through 891 removed outlier: 4.191A pdb=" N LEU E 878 " --> pdb=" O CYS E 874 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA E 891 " --> pdb=" O GLY E 887 " (cutoff:3.500A) Processing helix chain 'E' and resid 900 through 918 removed outlier: 3.537A pdb=" N LEU E 904 " --> pdb=" O SER E 900 " (cutoff:3.500A) Processing helix chain 'E' and resid 921 through 926 Processing helix chain 'E' and resid 927 through 934 removed outlier: 3.704A pdb=" N PHE E 931 " --> pdb=" O HIS E 928 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER E 932 " --> pdb=" O GLU E 929 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 934 " --> pdb=" O PHE E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 935 through 953 Processing helix chain 'E' and resid 982 through 995 Processing helix chain 'E' and resid 995 through 1004 removed outlier: 3.550A pdb=" N GLY E1000 " --> pdb=" O ILE E 996 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU E1001 " --> pdb=" O ASP E 997 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE E1002 " --> pdb=" O ARG E 998 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY E1004 " --> pdb=" O GLY E1000 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 16 removed outlier: 3.584A pdb=" N MET F 14 " --> pdb=" O SER F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 41 removed outlier: 3.716A pdb=" N ARG F 41 " --> pdb=" O LYS F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 48 removed outlier: 3.635A pdb=" N ARG F 46 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 79 Processing helix chain 'F' and resid 87 through 107 Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 195 through 204 removed outlier: 4.299A pdb=" N MET F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 227 Processing helix chain 'F' and resid 332 through 341 Processing helix chain 'F' and resid 385 through 399 Proline residue: F 391 - end of helix Processing helix chain 'F' and resid 405 through 419 Processing helix chain 'F' and resid 420 through 422 No H-bonds generated for 'chain 'F' and resid 420 through 422' Processing helix chain 'F' and resid 423 through 435 Processing helix chain 'F' and resid 449 through 474 Processing helix chain 'F' and resid 551 through 565 Processing helix chain 'F' and resid 584 through 588 removed outlier: 3.542A pdb=" N MET F 587 " --> pdb=" O ILE F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 597 Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.766A pdb=" N LEU G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU G 29 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY G 32 " --> pdb=" O GLU G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 46 Processing helix chain 'G' and resid 47 through 55 removed outlier: 3.769A pdb=" N LEU G 51 " --> pdb=" O ARG G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 74 removed outlier: 3.514A pdb=" N LYS G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 90 Processing helix chain 'G' and resid 100 through 109 Processing helix chain 'G' and resid 115 through 128 Processing helix chain 'G' and resid 136 through 147 Processing helix chain 'G' and resid 151 through 169 removed outlier: 4.094A pdb=" N ALA G 157 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE G 160 " --> pdb=" O GLU G 156 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 185 removed outlier: 3.876A pdb=" N GLY G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN G 178 " --> pdb=" O VAL G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 198 removed outlier: 3.514A pdb=" N LYS G 196 " --> pdb=" O ASP G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 204 removed outlier: 3.868A pdb=" N MET G 204 " --> pdb=" O LEU G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 225 removed outlier: 3.727A pdb=" N GLN G 220 " --> pdb=" O GLN G 216 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR G 223 " --> pdb=" O GLN G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 245 removed outlier: 3.652A pdb=" N HIS G 236 " --> pdb=" O ILE G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 262 Processing helix chain 'G' and resid 265 through 283 removed outlier: 3.984A pdb=" N LEU G 278 " --> pdb=" O GLN G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 302 removed outlier: 3.810A pdb=" N ILE G 292 " --> pdb=" O SER G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 321 removed outlier: 4.027A pdb=" N THR G 321 " --> pdb=" O THR G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 328 removed outlier: 3.507A pdb=" N HIS G 326 " --> pdb=" O ILE G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 354 removed outlier: 3.921A pdb=" N LYS G 346 " --> pdb=" O SER G 342 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR G 353 " --> pdb=" O GLN G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 374 removed outlier: 3.681A pdb=" N VAL G 366 " --> pdb=" O HIS G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 399 removed outlier: 3.627A pdb=" N GLN G 384 " --> pdb=" O LEU G 380 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU G 391 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER G 392 " --> pdb=" O PHE G 388 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLN G 399 " --> pdb=" O VAL G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 423 Processing helix chain 'G' and resid 426 through 441 removed outlier: 3.530A pdb=" N THR G 433 " --> pdb=" O SER G 429 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS G 439 " --> pdb=" O LEU G 435 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER G 440 " --> pdb=" O THR G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 458 Processing helix chain 'G' and resid 460 through 464 Processing helix chain 'G' and resid 467 through 477 removed outlier: 3.880A pdb=" N LEU G 471 " --> pdb=" O MET G 467 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET G 472 " --> pdb=" O LEU G 468 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL G 477 " --> pdb=" O GLU G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.870A pdb=" N ALA G 482 " --> pdb=" O ILE G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 501 removed outlier: 3.892A pdb=" N LEU G 489 " --> pdb=" O LYS G 485 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 519 Processing helix chain 'G' and resid 522 through 537 Processing helix chain 'G' and resid 538 through 551 removed outlier: 3.767A pdb=" N ALA G 542 " --> pdb=" O ASN G 538 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU G 544 " --> pdb=" O ASP G 540 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR G 551 " --> pdb=" O GLN G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 555 through 577 removed outlier: 3.546A pdb=" N TYR G 559 " --> pdb=" O SER G 555 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY G 577 " --> pdb=" O GLN G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 608 removed outlier: 3.543A pdb=" N ALA G 586 " --> pdb=" O ASN G 582 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU G 587 " --> pdb=" O TYR G 583 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER G 588 " --> pdb=" O SER G 584 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS G 599 " --> pdb=" O LYS G 595 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 641 Processing helix chain 'G' and resid 644 through 653 removed outlier: 4.115A pdb=" N ALA G 648 " --> pdb=" O SER G 644 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE G 649 " --> pdb=" O PRO G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 666 through 693 removed outlier: 4.036A pdb=" N GLN G 670 " --> pdb=" O ARG G 666 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE G 693 " --> pdb=" O TYR G 689 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 721 Processing helix chain 'G' and resid 723 through 728 removed outlier: 3.656A pdb=" N ALA G 727 " --> pdb=" O ASP G 723 " (cutoff:3.500A) Processing helix chain 'G' and resid 742 through 762 removed outlier: 3.598A pdb=" N SER G 761 " --> pdb=" O GLU G 757 " (cutoff:3.500A) Processing helix chain 'G' and resid 772 through 787 removed outlier: 3.804A pdb=" N VAL G 787 " --> pdb=" O ALA G 783 " (cutoff:3.500A) Processing helix chain 'G' and resid 792 through 796 Processing helix chain 'G' and resid 933 through 943 Processing helix chain 'H' and resid 23 through 30 removed outlier: 4.172A pdb=" N PHE H 27 " --> pdb=" O CYS H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 40 removed outlier: 3.771A pdb=" N GLU H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 60 Processing helix chain 'H' and resid 75 through 93 Processing helix chain 'H' and resid 95 through 103 Processing helix chain 'H' and resid 104 through 119 Processing helix chain 'H' and resid 126 through 130 Processing helix chain 'H' and resid 136 through 159 Processing helix chain 'H' and resid 170 through 194 removed outlier: 3.578A pdb=" N ASN H 175 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 206 Processing helix chain 'H' and resid 248 through 265 Processing helix chain 'H' and resid 266 through 268 No H-bonds generated for 'chain 'H' and resid 266 through 268' Processing helix chain 'H' and resid 269 through 289 removed outlier: 4.032A pdb=" N ASN H 273 " --> pdb=" O ALA H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 292 No H-bonds generated for 'chain 'H' and resid 290 through 292' Processing helix chain 'H' and resid 298 through 311 removed outlier: 3.844A pdb=" N LEU H 302 " --> pdb=" O ASP H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 336 Processing helix chain 'H' and resid 337 through 352 removed outlier: 3.798A pdb=" N LEU H 350 " --> pdb=" O ILE H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 373 removed outlier: 3.515A pdb=" N GLY H 373 " --> pdb=" O LYS H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 396 removed outlier: 4.226A pdb=" N ILE H 380 " --> pdb=" O ALA H 376 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU H 395 " --> pdb=" O ARG H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 400 through 407 removed outlier: 3.748A pdb=" N ASN H 404 " --> pdb=" O SER H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 426 Processing helix chain 'H' and resid 432 through 450 Processing helix chain 'H' and resid 452 through 462 Processing helix chain 'H' and resid 462 through 469 Processing helix chain 'H' and resid 470 through 483 Processing helix chain 'H' and resid 504 through 519 Processing helix chain 'H' and resid 521 through 536 Processing helix chain 'H' and resid 551 through 560 removed outlier: 4.110A pdb=" N GLY H 556 " --> pdb=" O SER H 552 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL H 557 " --> pdb=" O VAL H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 563 through 584 Processing helix chain 'H' and resid 585 through 602 removed outlier: 3.636A pdb=" N GLN H 591 " --> pdb=" O SER H 587 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU H 598 " --> pdb=" O ALA H 594 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU H 602 " --> pdb=" O GLU H 598 " (cutoff:3.500A) Processing helix chain 'H' and resid 604 through 626 removed outlier: 3.649A pdb=" N ARG H 608 " --> pdb=" O SER H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 636 through 649 removed outlier: 3.614A pdb=" N ARG H 649 " --> pdb=" O TYR H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 656 through 670 Processing helix chain 'H' and resid 688 through 704 Processing helix chain 'H' and resid 711 through 726 Processing helix chain 'H' and resid 753 through 763 Processing helix chain 'H' and resid 766 through 783 Processing helix chain 'H' and resid 810 through 829 Processing helix chain 'H' and resid 832 through 846 Processing helix chain 'H' and resid 848 through 864 Processing helix chain 'H' and resid 877 through 891 Processing helix chain 'H' and resid 895 through 902 removed outlier: 3.904A pdb=" N GLN H 902 " --> pdb=" O ALA H 898 " (cutoff:3.500A) Processing helix chain 'H' and resid 908 through 918 removed outlier: 4.430A pdb=" N GLU H 918 " --> pdb=" O LYS H 914 " (cutoff:3.500A) Processing helix chain 'H' and resid 926 through 931 removed outlier: 3.761A pdb=" N ASP H 930 " --> pdb=" O SER H 927 " (cutoff:3.500A) Processing helix chain 'H' and resid 934 through 949 Processing helix chain 'H' and resid 950 through 963 removed outlier: 4.062A pdb=" N ILE H 956 " --> pdb=" O ASP H 952 " (cutoff:3.500A) Processing helix chain 'H' and resid 972 through 994 removed outlier: 3.625A pdb=" N LEU H 977 " --> pdb=" O GLU H 973 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 38 Processing helix chain 'I' and resid 46 through 51 Processing helix chain 'I' and resid 92 through 96 Processing helix chain 'I' and resid 109 through 117 removed outlier: 4.000A pdb=" N ILE I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR I 117 " --> pdb=" O ILE I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 145 Processing helix chain 'I' and resid 154 through 157 Processing helix chain 'I' and resid 158 through 165 removed outlier: 3.671A pdb=" N LEU I 164 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 172 Processing helix chain 'I' and resid 174 through 178 removed outlier: 3.633A pdb=" N TRP I 178 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 193 Processing helix chain 'I' and resid 252 through 256 removed outlier: 3.599A pdb=" N LYS I 256 " --> pdb=" O ALA I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 292 Processing helix chain 'I' and resid 303 through 320 removed outlier: 4.174A pdb=" N ASP I 307 " --> pdb=" O GLY I 303 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP I 317 " --> pdb=" O TYR I 313 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER I 318 " --> pdb=" O GLN I 314 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA I 319 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 343 Processing helix chain 'I' and resid 348 through 357 Processing helix chain 'I' and resid 363 through 371 Processing helix chain 'I' and resid 381 through 386 removed outlier: 3.717A pdb=" N ASN I 385 " --> pdb=" O GLY I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 413 removed outlier: 4.211A pdb=" N HIS I 407 " --> pdb=" O GLY I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 434 Processing helix chain 'I' and resid 435 through 437 No H-bonds generated for 'chain 'I' and resid 435 through 437' Processing helix chain 'I' and resid 453 through 465 Processing helix chain 'I' and resid 472 through 477 removed outlier: 3.614A pdb=" N THR I 476 " --> pdb=" O PRO I 472 " (cutoff:3.500A) Processing helix chain 'I' and resid 479 through 483 removed outlier: 4.154A pdb=" N SER I 483 " --> pdb=" O PRO I 480 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 526 Processing helix chain 'I' and resid 590 through 602 Processing helix chain 'I' and resid 621 through 623 No H-bonds generated for 'chain 'I' and resid 621 through 623' Processing helix chain 'I' and resid 641 through 653 removed outlier: 3.792A pdb=" N LYS I 653 " --> pdb=" O ASP I 649 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 45 Processing helix chain 'K' and resid 56 through 61 removed outlier: 4.080A pdb=" N PHE K 60 " --> pdb=" O ARG K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 76 through 82 Processing helix chain 'K' and resid 94 through 115 Proline residue: K 101 - end of helix Processing helix chain 'K' and resid 122 through 132 removed outlier: 3.625A pdb=" N LYS K 132 " --> pdb=" O ASP K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 231 Processing helix chain 'K' and resid 243 through 260 Processing helix chain 'K' and resid 271 through 282 removed outlier: 4.092A pdb=" N HIS K 277 " --> pdb=" O GLU K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 285 No H-bonds generated for 'chain 'K' and resid 283 through 285' Processing helix chain 'K' and resid 286 through 294 removed outlier: 4.115A pdb=" N ILE K 290 " --> pdb=" O THR K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 315 removed outlier: 3.852A pdb=" N ASP K 314 " --> pdb=" O ALA K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 341 removed outlier: 3.788A pdb=" N ILE K 336 " --> pdb=" O GLN K 332 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 365 Processing helix chain 'K' and resid 394 through 406 Processing helix chain 'K' and resid 416 through 432 Processing helix chain 'K' and resid 458 through 470 Processing helix chain 'K' and resid 494 through 503 Processing helix chain 'K' and resid 525 through 538 Processing helix chain 'K' and resid 580 through 593 removed outlier: 3.658A pdb=" N LYS K 593 " --> pdb=" O SER K 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 655 through 670 Processing helix chain 'P' and resid 10 through 21 removed outlier: 3.538A pdb=" N ASP P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 43 removed outlier: 4.428A pdb=" N SER P 36 " --> pdb=" O ILE P 32 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR P 37 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 58 removed outlier: 4.723A pdb=" N LEU P 52 " --> pdb=" O ARG P 48 " (cutoff:3.500A) Proline residue: P 53 - end of helix Processing helix chain 'P' and resid 63 through 76 removed outlier: 3.838A pdb=" N GLY P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR P 75 " --> pdb=" O GLU P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 81 Processing helix chain 'P' and resid 82 through 84 No H-bonds generated for 'chain 'P' and resid 82 through 84' Processing helix chain 'P' and resid 85 through 98 removed outlier: 3.884A pdb=" N LEU P 89 " --> pdb=" O TYR P 85 " (cutoff:3.500A) Proline residue: P 91 - end of helix removed outlier: 3.739A pdb=" N THR P 98 " --> pdb=" O GLU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 119 Processing helix chain 'P' and resid 120 through 127 Processing helix chain 'P' and resid 127 through 138 removed outlier: 3.556A pdb=" N ARG P 134 " --> pdb=" O PRO P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 149 removed outlier: 3.855A pdb=" N GLY P 149 " --> pdb=" O THR P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 155 removed outlier: 4.448A pdb=" N VAL P 153 " --> pdb=" O GLY P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 175 Processing helix chain 'P' and resid 178 through 196 removed outlier: 4.346A pdb=" N ALA P 184 " --> pdb=" O MET P 180 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU P 191 " --> pdb=" O SER P 187 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS P 194 " --> pdb=" O GLY P 190 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL P 195 " --> pdb=" O GLU P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 204 Processing helix chain 'P' and resid 204 through 215 Processing helix chain 'P' and resid 217 through 235 removed outlier: 3.680A pdb=" N LEU P 223 " --> pdb=" O SER P 219 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU P 226 " --> pdb=" O LEU P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 253 removed outlier: 3.746A pdb=" N LEU P 240 " --> pdb=" O PRO P 236 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU P 241 " --> pdb=" O GLN P 237 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA P 242 " --> pdb=" O GLU P 238 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU P 243 " --> pdb=" O ASP P 239 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N MET P 245 " --> pdb=" O GLU P 241 " (cutoff:3.500A) Proline residue: P 246 - end of helix removed outlier: 3.695A pdb=" N GLU P 253 " --> pdb=" O ARG P 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 266 removed outlier: 4.159A pdb=" N ARG P 260 " --> pdb=" O SER P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 275 Processing helix chain 'P' and resid 275 through 282 Processing helix chain 'P' and resid 282 through 292 removed outlier: 3.860A pdb=" N ALA P 286 " --> pdb=" O ASP P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 305 removed outlier: 3.669A pdb=" N LYS P 305 " --> pdb=" O ALA P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 305 through 312 Processing helix chain 'P' and resid 317 through 325 Processing helix chain 'P' and resid 325 through 336 Processing helix chain 'P' and resid 338 through 350 removed outlier: 3.567A pdb=" N LYS P 342 " --> pdb=" O ASN P 338 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER P 347 " --> pdb=" O SER P 343 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL P 348 " --> pdb=" O ALA P 344 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET P 350 " --> pdb=" O ALA P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 352 through 357 removed outlier: 3.790A pdb=" N LEU P 356 " --> pdb=" O LEU P 352 " (cutoff:3.500A) Processing helix chain 'P' and resid 357 through 374 removed outlier: 4.718A pdb=" N LEU P 366 " --> pdb=" O ILE P 362 " (cutoff:3.500A) Proline residue: P 367 - end of helix Processing helix chain 'P' and resid 377 through 387 removed outlier: 3.562A pdb=" N ARG P 381 " --> pdb=" O CYS P 377 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN P 387 " --> pdb=" O ASN P 383 " (cutoff:3.500A) Processing helix chain 'P' and resid 387 through 395 removed outlier: 4.334A pdb=" N VAL P 391 " --> pdb=" O ASN P 387 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN P 392 " --> pdb=" O LEU P 388 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU P 393 " --> pdb=" O ASP P 389 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL P 394 " --> pdb=" O CYS P 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 396 through 413 removed outlier: 3.779A pdb=" N LEU P 400 " --> pdb=" O GLY P 396 " (cutoff:3.500A) Proline residue: P 406 - end of helix removed outlier: 4.501A pdb=" N VAL P 409 " --> pdb=" O LEU P 405 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLU P 410 " --> pdb=" O PRO P 406 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU P 413 " --> pdb=" O VAL P 409 " (cutoff:3.500A) Processing helix chain 'P' and resid 416 through 442 removed outlier: 3.921A pdb=" N ARG P 420 " --> pdb=" O LYS P 416 " (cutoff:3.500A) Proline residue: P 428 - end of helix removed outlier: 6.320A pdb=" N VAL P 436 " --> pdb=" O GLY P 432 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N GLU P 437 " --> pdb=" O GLN P 433 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE P 438 " --> pdb=" O LEU P 434 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE P 439 " --> pdb=" O GLY P 435 " (cutoff:3.500A) Processing helix chain 'P' and resid 442 through 451 removed outlier: 3.646A pdb=" N LEU P 446 " --> pdb=" O LYS P 442 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 474 removed outlier: 3.798A pdb=" N ARG P 459 " --> pdb=" O VAL P 455 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU P 471 " --> pdb=" O LYS P 467 " (cutoff:3.500A) Processing helix chain 'P' and resid 474 through 487 removed outlier: 4.783A pdb=" N ILE P 483 " --> pdb=" O HIS P 479 " (cutoff:3.500A) Proline residue: P 484 - end of helix Processing helix chain 'P' and resid 488 through 490 No H-bonds generated for 'chain 'P' and resid 488 through 490' Processing helix chain 'P' and resid 495 through 509 removed outlier: 3.693A pdb=" N LEU P 502 " --> pdb=" O ARG P 498 " (cutoff:3.500A) Processing helix chain 'P' and resid 514 through 528 removed outlier: 4.244A pdb=" N LEU P 522 " --> pdb=" O THR P 518 " (cutoff:3.500A) Proline residue: P 523 - end of helix Processing helix chain 'P' and resid 529 through 531 No H-bonds generated for 'chain 'P' and resid 529 through 531' Processing helix chain 'P' and resid 533 through 548 removed outlier: 3.817A pdb=" N ALA P 541 " --> pdb=" O ARG P 537 " (cutoff:3.500A) Processing helix chain 'P' and resid 549 through 551 No H-bonds generated for 'chain 'P' and resid 549 through 551' Processing helix chain 'P' and resid 552 through 570 removed outlier: 4.876A pdb=" N LYS P 561 " --> pdb=" O GLN P 557 " (cutoff:3.500A) Proline residue: P 562 - end of helix removed outlier: 3.531A pdb=" N ASP P 570 " --> pdb=" O LYS P 566 " (cutoff:3.500A) Processing helix chain 'P' and resid 572 through 587 Processing helix chain 'Q' and resid 3 through 18 Processing helix chain 'Q' and resid 24 through 40 removed outlier: 3.737A pdb=" N GLU Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 73 Processing helix chain 'Q' and resid 92 through 107 Processing helix chain 'Q' and resid 120 through 127 removed outlier: 3.775A pdb=" N THR Q 124 " --> pdb=" O SER Q 120 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN Q 125 " --> pdb=" O ARG Q 121 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL Q 126 " --> pdb=" O GLN Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 138 Processing helix chain 'Q' and resid 140 through 150 removed outlier: 3.565A pdb=" N ASP Q 148 " --> pdb=" O LYS Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 151 through 153 No H-bonds generated for 'chain 'Q' and resid 151 through 153' Processing helix chain 'Q' and resid 176 through 183 Processing helix chain 'Q' and resid 193 through 199 removed outlier: 3.818A pdb=" N LEU Q 199 " --> pdb=" O MET Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 221 through 233 Processing helix chain 'Q' and resid 264 through 268 Processing helix chain 'U' and resid 507 through 511 removed outlier: 3.721A pdb=" N UNK U 511 " --> pdb=" O UNK U 508 " (cutoff:3.500A) Processing helix chain 'U' and resid 512 through 523 removed outlier: 3.532A pdb=" N UNK U 521 " --> pdb=" O UNK U 517 " (cutoff:3.500A) Processing helix chain '1' and resid 27 through 35 Processing helix chain '1' and resid 98 through 110 removed outlier: 4.189A pdb=" N LYS 1 102 " --> pdb=" O GLY 1 98 " (cutoff:3.500A) Processing helix chain '1' and resid 123 through 133 Processing helix chain '1' and resid 136 through 149 Processing helix chain '1' and resid 217 through 228 Processing helix chain '1' and resid 229 through 236 Processing helix chain '1' and resid 244 through 249 removed outlier: 3.742A pdb=" N MET 1 248 " --> pdb=" O ARG 1 244 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE 1 249 " --> pdb=" O PRO 1 245 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 244 through 249' Processing helix chain '1' and resid 274 through 296 removed outlier: 3.697A pdb=" N HIS 1 278 " --> pdb=" O ASP 1 274 " (cutoff:3.500A) Processing helix chain '1' and resid 301 through 319 Processing helix chain '1' and resid 338 through 345 removed outlier: 4.010A pdb=" N GLY 1 345 " --> pdb=" O GLN 1 341 " (cutoff:3.500A) Processing helix chain '1' and resid 382 through 388 Processing helix chain '1' and resid 395 through 407 removed outlier: 4.667A pdb=" N ASP 1 400 " --> pdb=" O PRO 1 396 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG 1 401 " --> pdb=" O PHE 1 397 " (cutoff:3.500A) Processing helix chain '1' and resid 434 through 439 Processing helix chain '1' and resid 465 through 469 removed outlier: 3.697A pdb=" N MET 1 469 " --> pdb=" O LYS 1 466 " (cutoff:3.500A) Processing helix chain '1' and resid 488 through 493 removed outlier: 3.541A pdb=" N TYR 1 492 " --> pdb=" O VAL 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 508 through 519 Processing helix chain '1' and resid 520 through 525 removed outlier: 3.834A pdb=" N ILE 1 525 " --> pdb=" O PRO 1 522 " (cutoff:3.500A) Processing helix chain '1' and resid 538 through 549 Processing helix chain '1' and resid 556 through 564 Processing helix chain '1' and resid 565 through 567 No H-bonds generated for 'chain '1' and resid 565 through 567' Processing helix chain '1' and resid 587 through 596 Processing helix chain '1' and resid 610 through 616 removed outlier: 4.314A pdb=" N ASP 1 614 " --> pdb=" O PRO 1 610 " (cutoff:3.500A) Processing helix chain '1' and resid 641 through 646 Processing helix chain '1' and resid 651 through 660 Processing helix chain '1' and resid 661 through 684 removed outlier: 3.877A pdb=" N ILE 1 682 " --> pdb=" O ASN 1 678 " (cutoff:3.500A) Processing helix chain '1' and resid 688 through 693 Processing helix chain '1' and resid 695 through 722 Processing helix chain '1' and resid 732 through 759 removed outlier: 3.794A pdb=" N SER 1 759 " --> pdb=" O SER 1 755 " (cutoff:3.500A) Processing helix chain '1' and resid 764 through 773 Processing helix chain '1' and resid 777 through 785 removed outlier: 4.147A pdb=" N ILE 1 781 " --> pdb=" O SER 1 777 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER 1 782 " --> pdb=" O LYS 1 778 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN 1 783 " --> pdb=" O ILE 1 779 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL 1 784 " --> pdb=" O ASN 1 780 " (cutoff:3.500A) Processing helix chain '1' and resid 816 through 821 Processing helix chain '1' and resid 826 through 830 Processing helix chain '1' and resid 832 through 868 removed outlier: 3.918A pdb=" N ASP 1 849 " --> pdb=" O GLU 1 845 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR 1 850 " --> pdb=" O GLY 1 846 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA 1 855 " --> pdb=" O ALA 1 851 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU 1 856 " --> pdb=" O VAL 1 852 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY 1 858 " --> pdb=" O THR 1 854 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR 1 859 " --> pdb=" O ALA 1 855 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 1 864 " --> pdb=" O ILE 1 860 " (cutoff:3.500A) Processing helix chain '1' and resid 890 through 894 Processing helix chain '1' and resid 912 through 921 Processing helix chain '1' and resid 926 through 934 Processing helix chain '1' and resid 935 through 945 Processing helix chain '1' and resid 945 through 970 removed outlier: 3.749A pdb=" N GLN 1 949 " --> pdb=" O ASN 1 945 " (cutoff:3.500A) Processing helix chain '1' and resid 982 through 995 Processing helix chain '1' and resid 1005 through 1020 removed outlier: 3.636A pdb=" N VAL 11009 " --> pdb=" O HIS 11005 " (cutoff:3.500A) Processing helix chain '1' and resid 1027 through 1038 Processing helix chain '1' and resid 1038 through 1049 Processing helix chain '1' and resid 1050 through 1057 Processing helix chain '1' and resid 1061 through 1079 Processing helix chain '1' and resid 1086 through 1102 removed outlier: 3.605A pdb=" N LEU 11090 " --> pdb=" O MET 11086 " (cutoff:3.500A) Proline residue: 11098 - end of helix Processing helix chain '1' and resid 1103 through 1107 removed outlier: 4.293A pdb=" N PHE 11107 " --> pdb=" O LEU 11104 " (cutoff:3.500A) Processing helix chain '1' and resid 1120 through 1129 Processing helix chain '1' and resid 1145 through 1150 Processing helix chain '1' and resid 1150 through 1162 Processing helix chain '1' and resid 1165 through 1169 Processing helix chain '1' and resid 1189 through 1195 removed outlier: 3.662A pdb=" N VAL 11193 " --> pdb=" O ASP 11189 " (cutoff:3.500A) Processing helix chain '1' and resid 1217 through 1225 Processing helix chain '1' and resid 1227 through 1239 removed outlier: 3.522A pdb=" N ILE 11231 " --> pdb=" O THR 11227 " (cutoff:3.500A) Processing helix chain '1' and resid 1281 through 1296 removed outlier: 3.709A pdb=" N MET 11296 " --> pdb=" O MET 11292 " (cutoff:3.500A) Processing helix chain '1' and resid 1362 through 1369 removed outlier: 3.503A pdb=" N VAL 11368 " --> pdb=" O GLU 11364 " (cutoff:3.500A) Processing helix chain '1' and resid 1371 through 1387 Processing helix chain '1' and resid 1394 through 1407 removed outlier: 3.899A pdb=" N LEU 11398 " --> pdb=" O ASN 11394 " (cutoff:3.500A) Processing helix chain '1' and resid 1415 through 1420 Processing helix chain '1' and resid 1425 through 1432 Processing helix chain '1' and resid 1435 through 1445 Processing helix chain '1' and resid 1453 through 1460 Processing helix chain '1' and resid 1476 through 1481 Processing helix chain '2' and resid 21 through 38 Processing helix chain '2' and resid 40 through 53 Processing helix chain '2' and resid 53 through 62 Processing helix chain '2' and resid 109 through 116 removed outlier: 3.504A pdb=" N ARG 2 116 " --> pdb=" O GLU 2 112 " (cutoff:3.500A) Processing helix chain '2' and resid 167 through 174 Processing helix chain '2' and resid 269 through 277 Processing helix chain '2' and resid 280 through 289 removed outlier: 4.160A pdb=" N ILE 2 284 " --> pdb=" O SER 2 280 " (cutoff:3.500A) Processing helix chain '2' and resid 294 through 306 removed outlier: 3.554A pdb=" N MET 2 300 " --> pdb=" O GLU 2 296 " (cutoff:3.500A) Proline residue: 2 303 - end of helix Processing helix chain '2' and resid 307 through 311 removed outlier: 4.239A pdb=" N VAL 2 310 " --> pdb=" O GLU 2 307 " (cutoff:3.500A) Processing helix chain '2' and resid 313 through 323 Processing helix chain '2' and resid 331 through 346 removed outlier: 3.572A pdb=" N ARG 2 335 " --> pdb=" O THR 2 331 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS 2 337 " --> pdb=" O GLU 2 333 " (cutoff:3.500A) Processing helix chain '2' and resid 348 through 352 Processing helix chain '2' and resid 357 through 378 Processing helix chain '2' and resid 387 through 389 No H-bonds generated for 'chain '2' and resid 387 through 389' Processing helix chain '2' and resid 395 through 425 removed outlier: 3.617A pdb=" N LEU 2 399 " --> pdb=" O LEU 2 395 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET 2 407 " --> pdb=" O LEU 2 403 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG 2 425 " --> pdb=" O LYS 2 421 " (cutoff:3.500A) Processing helix chain '2' and resid 430 through 435 Processing helix chain '2' and resid 437 through 450 removed outlier: 4.504A pdb=" N GLY 2 443 " --> pdb=" O ILE 2 439 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU 2 444 " --> pdb=" O ILE 2 440 " (cutoff:3.500A) Processing helix chain '2' and resid 474 through 483 Processing helix chain '2' and resid 495 through 500 removed outlier: 4.325A pdb=" N ARG 2 499 " --> pdb=" O LEU 2 495 " (cutoff:3.500A) Processing helix chain '2' and resid 538 through 548 Processing helix chain '2' and resid 583 through 593 Processing helix chain '2' and resid 636 through 645 removed outlier: 4.028A pdb=" N ILE 2 640 " --> pdb=" O LYS 2 636 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU 2 645 " --> pdb=" O ASP 2 641 " (cutoff:3.500A) Processing helix chain '2' and resid 652 through 660 Processing helix chain '2' and resid 667 through 671 Processing helix chain '2' and resid 699 through 704 removed outlier: 3.522A pdb=" N LEU 2 704 " --> pdb=" O SER 2 701 " (cutoff:3.500A) Processing helix chain '2' and resid 707 through 711 removed outlier: 3.579A pdb=" N ILE 2 710 " --> pdb=" O CYS 2 707 " (cutoff:3.500A) Processing helix chain '2' and resid 713 through 717 Processing helix chain '2' and resid 718 through 729 Processing helix chain '2' and resid 762 through 768 removed outlier: 3.855A pdb=" N GLU 2 765 " --> pdb=" O ARG 2 762 " (cutoff:3.500A) Processing helix chain '2' and resid 798 through 804 Processing helix chain '2' and resid 971 through 976 Processing helix chain '2' and resid 977 through 994 removed outlier: 4.026A pdb=" N LEU 2 981 " --> pdb=" O THR 2 977 " (cutoff:3.500A) Processing helix chain '2' and resid 1007 through 1019 Processing helix chain '2' and resid 1054 through 1058 removed outlier: 3.570A pdb=" N ASP 21057 " --> pdb=" O MET 21054 " (cutoff:3.500A) Processing helix chain '2' and resid 1077 through 1081 Processing helix chain '2' and resid 1087 through 1098 Processing helix chain '2' and resid 1099 through 1108 Processing helix chain '2' and resid 1152 through 1165 removed outlier: 3.587A pdb=" N GLN 21160 " --> pdb=" O LYS 21156 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU 21161 " --> pdb=" O LEU 21157 " (cutoff:3.500A) Processing helix chain '3' and resid 27 through 41 removed outlier: 3.547A pdb=" N PHE 3 38 " --> pdb=" O ILE 3 34 " (cutoff:3.500A) Processing helix chain '3' and resid 60 through 71 removed outlier: 3.588A pdb=" N ILE 3 71 " --> pdb=" O ARG 3 67 " (cutoff:3.500A) Processing helix chain '3' and resid 77 through 82 removed outlier: 3.884A pdb=" N LYS 3 81 " --> pdb=" O ASP 3 77 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 240 through 271 Processing helix chain '4' and resid 3 through 25 Processing helix chain '4' and resid 29 through 34 Processing helix chain '4' and resid 36 through 45 Processing helix chain '4' and resid 83 through 97 Processing helix chain '4' and resid 111 through 122 Processing helix chain '4' and resid 132 through 136 Processing helix chain '4' and resid 152 through 164 removed outlier: 3.597A pdb=" N GLU 4 158 " --> pdb=" O GLU 4 154 " (cutoff:3.500A) Processing helix chain '4' and resid 166 through 170 Processing helix chain '4' and resid 177 through 184 Processing helix chain '5' and resid 58 through 75 Processing helix chain '5' and resid 88 through 100 removed outlier: 4.013A pdb=" N ILE 5 92 " --> pdb=" O ASP 5 88 " (cutoff:3.500A) Processing helix chain '6' and resid 83 through 87 Processing helix chain '6' and resid 129 through 133 Processing helix chain '7' and resid 63 through 68 removed outlier: 4.053A pdb=" N GLN 7 67 " --> pdb=" O ASP 7 63 " (cutoff:3.500A) Processing helix chain '7' and resid 69 through 75 removed outlier: 3.917A pdb=" N VAL 7 72 " --> pdb=" O ILE 7 69 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN 7 74 " --> pdb=" O ASP 7 71 " (cutoff:3.500A) Processing helix chain '8' and resid 16 through 27 removed outlier: 4.660A pdb=" N ALA 8 20 " --> pdb=" O ASN 8 16 " (cutoff:3.500A) Processing helix chain '8' and resid 30 through 39 Processing helix chain '8' and resid 42 through 51 removed outlier: 3.585A pdb=" N ARG 8 47 " --> pdb=" O TYR 8 43 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N MET 8 48 " --> pdb=" O CYS 8 44 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU 8 49 " --> pdb=" O CYS 8 45 " (cutoff:3.500A) Processing helix chain '8' and resid 55 through 61 Processing helix chain '9' and resid 5 through 10 Processing helix chain '9' and resid 39 through 51 removed outlier: 3.684A pdb=" N GLY 9 43 " --> pdb=" O ASP 9 39 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN 9 44 " --> pdb=" O HIS 9 40 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE 9 45 " --> pdb=" O THR 9 41 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS 9 47 " --> pdb=" O GLY 9 43 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 115 Processing helix chain 'e' and resid 8 through 17 Processing helix chain 'e' and resid 28 through 33 Processing helix chain 'e' and resid 34 through 40 Processing helix chain 'e' and resid 49 through 63 Processing helix chain 'e' and resid 64 through 71 Processing helix chain 'e' and resid 71 through 85 removed outlier: 3.941A pdb=" N LEU e 75 " --> pdb=" O MET e 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 87 through 98 Processing helix chain 'e' and resid 98 through 104 removed outlier: 4.246A pdb=" N ASP e 102 " --> pdb=" O LYS e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 114 through 131 removed outlier: 3.645A pdb=" N GLN e 118 " --> pdb=" O ASN e 114 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU e 126 " --> pdb=" O GLY e 122 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 144 removed outlier: 3.680A pdb=" N GLN e 142 " --> pdb=" O PRO e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 145 through 154 Processing helix chain 'e' and resid 169 through 188 removed outlier: 4.106A pdb=" N GLN e 188 " --> pdb=" O GLU e 184 " (cutoff:3.500A) Processing helix chain 'f' and resid 7 through 20 Processing helix chain 'f' and resid 26 through 35 removed outlier: 4.070A pdb=" N THR f 35 " --> pdb=" O GLU f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 52 Proline residue: f 49 - end of helix Processing helix chain 'f' and resid 57 through 82 Processing helix chain 'f' and resid 85 through 103 Processing helix chain 'f' and resid 110 through 119 Processing helix chain 'f' and resid 125 through 133 Processing helix chain 'f' and resid 138 through 143 Processing helix chain 'f' and resid 155 through 177 Proline residue: f 163 - end of helix Processing helix chain 'f' and resid 200 through 209 removed outlier: 4.344A pdb=" N GLY f 209 " --> pdb=" O THR f 205 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 230 Processing helix chain 'f' and resid 231 through 247 removed outlier: 4.004A pdb=" N CYS f 235 " --> pdb=" O ASN f 231 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR f 236 " --> pdb=" O VAL f 232 " (cutoff:3.500A) Processing helix chain 'f' and resid 260 through 273 Processing helix chain 'f' and resid 277 through 289 Processing helix chain 'f' and resid 295 through 306 Processing helix chain 'f' and resid 307 through 329 Processing helix chain 'f' and resid 339 through 354 removed outlier: 4.335A pdb=" N MET f 354 " --> pdb=" O GLY f 350 " (cutoff:3.500A) Processing helix chain 'f' and resid 365 through 388 removed outlier: 3.575A pdb=" N ILE f 370 " --> pdb=" O GLU f 366 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR f 371 " --> pdb=" O VAL f 367 " (cutoff:3.500A) Proline residue: f 375 - end of helix Processing helix chain 'f' and resid 409 through 418 Processing helix chain 'f' and resid 420 through 432 Processing helix chain 'f' and resid 440 through 456 Proline residue: f 446 - end of helix Processing helix chain 'f' and resid 457 through 475 Processing helix chain 'f' and resid 476 through 494 Processing helix chain 'f' and resid 495 through 509 removed outlier: 3.847A pdb=" N LEU f 508 " --> pdb=" O ALA f 504 " (cutoff:3.500A) Processing helix chain 'f' and resid 515 through 528 removed outlier: 3.549A pdb=" N GLU f 528 " --> pdb=" O GLN f 524 " (cutoff:3.500A) Processing helix chain 'f' and resid 532 through 546 removed outlier: 3.590A pdb=" N ALA f 536 " --> pdb=" O GLN f 532 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 60 No H-bonds generated for 'chain 'g' and resid 58 through 60' Processing helix chain 'g' and resid 61 through 71 removed outlier: 3.655A pdb=" N LYS g 67 " --> pdb=" O PHE g 63 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN g 71 " --> pdb=" O LYS g 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 84 Processing helix chain 'g' and resid 90 through 105 removed outlier: 3.503A pdb=" N GLU g 99 " --> pdb=" O ASN g 95 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR g 104 " --> pdb=" O TRP g 100 " (cutoff:3.500A) Processing helix chain 'g' and resid 110 through 127 Processing helix chain 'g' and resid 132 through 140 removed outlier: 4.344A pdb=" N GLY g 140 " --> pdb=" O PHE g 136 " (cutoff:3.500A) Processing helix chain 'g' and resid 142 through 151 removed outlier: 3.722A pdb=" N LEU g 146 " --> pdb=" O THR g 142 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU g 147 " --> pdb=" O PRO g 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 155 through 164 removed outlier: 4.237A pdb=" N GLU g 164 " --> pdb=" O TYR g 160 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 182 Processing helix chain 'g' and resid 197 through 216 Processing helix chain 'g' and resid 217 through 221 removed outlier: 4.182A pdb=" N GLU g 221 " --> pdb=" O GLU g 218 " (cutoff:3.500A) Processing helix chain 'g' and resid 223 through 229 Processing helix chain 'g' and resid 234 through 251 removed outlier: 4.178A pdb=" N GLU g 251 " --> pdb=" O VAL g 247 " (cutoff:3.500A) Processing helix chain 'g' and resid 254 through 273 removed outlier: 3.553A pdb=" N GLU g 271 " --> pdb=" O ARG g 267 " (cutoff:3.500A) Processing helix chain 'g' and resid 276 through 284 Processing helix chain 'g' and resid 285 through 288 Processing helix chain 'g' and resid 289 through 303 Processing helix chain 'g' and resid 306 through 317 removed outlier: 3.623A pdb=" N VAL g 312 " --> pdb=" O ALA g 308 " (cutoff:3.500A) Processing helix chain 'g' and resid 324 through 328 Processing helix chain 'g' and resid 330 through 342 removed outlier: 3.516A pdb=" N LEU g 334 " --> pdb=" O VAL g 330 " (cutoff:3.500A) Processing helix chain 'g' and resid 352 through 366 removed outlier: 3.528A pdb=" N VAL g 366 " --> pdb=" O TYR g 362 " (cutoff:3.500A) Processing helix chain 'g' and resid 382 through 401 removed outlier: 3.753A pdb=" N GLU g 400 " --> pdb=" O LEU g 396 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASN g 401 " --> pdb=" O CYS g 397 " (cutoff:3.500A) Processing helix chain 'g' and resid 405 through 419 removed outlier: 4.233A pdb=" N SER g 412 " --> pdb=" O VAL g 408 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR g 413 " --> pdb=" O ALA g 409 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG g 419 " --> pdb=" O TYR g 415 " (cutoff:3.500A) Processing helix chain 'g' and resid 420 through 437 removed outlier: 3.671A pdb=" N GLU g 437 " --> pdb=" O TRP g 433 " (cutoff:3.500A) Processing helix chain 'g' and resid 448 through 462 removed outlier: 3.592A pdb=" N LEU g 452 " --> pdb=" O THR g 448 " (cutoff:3.500A) Processing helix chain 'g' and resid 465 through 479 Processing helix chain 'g' and resid 485 through 506 Processing helix chain 'g' and resid 509 through 522 Processing helix chain 'g' and resid 526 through 541 removed outlier: 3.733A pdb=" N ILE g 530 " --> pdb=" O ASP g 526 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP g 539 " --> pdb=" O THR g 535 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL g 540 " --> pdb=" O GLU g 536 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE g 541 " --> pdb=" O VAL g 537 " (cutoff:3.500A) Processing helix chain 'g' and resid 546 through 558 Proline residue: g 555 - end of helix Processing helix chain 'g' and resid 561 through 566 Processing helix chain 'g' and resid 573 through 586 removed outlier: 3.884A pdb=" N GLU g 577 " --> pdb=" O ASP g 573 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE g 578 " --> pdb=" O PRO g 574 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 19 removed outlier: 3.617A pdb=" N PHE h 19 " --> pdb=" O LEU h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 20 through 22 No H-bonds generated for 'chain 'h' and resid 20 through 22' Processing helix chain 'i' and resid 25 through 31 Processing helix chain 'i' and resid 36 through 41 Processing helix chain 'i' and resid 46 through 52 Processing helix chain 'i' and resid 65 through 68 Processing helix chain 'i' and resid 69 through 75 Processing helix chain 'i' and resid 94 through 105 Processing helix chain 'j' and resid 188 through 204 Processing helix chain 'j' and resid 231 through 240 Processing helix chain 'j' and resid 242 through 244 No H-bonds generated for 'chain 'j' and resid 242 through 244' Processing helix chain 'j' and resid 245 through 250 removed outlier: 3.835A pdb=" N TRP j 250 " --> pdb=" O ARG j 246 " (cutoff:3.500A) Processing helix chain 'j' and resid 256 through 258 No H-bonds generated for 'chain 'j' and resid 256 through 258' Processing helix chain 'j' and resid 259 through 264 removed outlier: 3.744A pdb=" N LEU j 264 " --> pdb=" O MET j 260 " (cutoff:3.500A) Processing helix chain 'j' and resid 341 through 349 Processing helix chain 'j' and resid 389 through 396 Processing helix chain 'j' and resid 514 through 516 No H-bonds generated for 'chain 'j' and resid 514 through 516' Processing helix chain 'j' and resid 630 through 633 Processing helix chain 'k' and resid 14 through 18 Processing helix chain 'k' and resid 21 through 35 removed outlier: 3.565A pdb=" N PHE k 31 " --> pdb=" O LYS k 27 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR k 32 " --> pdb=" O GLN k 28 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL k 34 " --> pdb=" O LEU k 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 23 through 28 Processing helix chain 'l' and resid 33 through 50 Processing helix chain 'l' and resid 58 through 71 removed outlier: 3.552A pdb=" N MET l 62 " --> pdb=" O SER l 58 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 90 removed outlier: 3.714A pdb=" N GLN l 89 " --> pdb=" O SER l 85 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS l 90 " --> pdb=" O LEU l 86 " (cutoff:3.500A) Processing helix chain 'l' and resid 93 through 104 Processing helix chain 'l' and resid 107 through 115 Processing helix chain 'l' and resid 116 through 119 Processing helix chain 'l' and resid 123 through 138 Processing sheet with id=AA1, first strand: chain 'A' and resid 728 through 730 Processing sheet with id=AA2, first strand: chain 'A' and resid 1159 through 1162 Processing sheet with id=AA3, first strand: chain 'D' and resid 821 through 826 removed outlier: 5.817A pdb=" N ALA D 822 " --> pdb=" O GLU D 852 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU D 852 " --> pdb=" O ALA D 822 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE D 824 " --> pdb=" O THR D 850 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR D 850 " --> pdb=" O ILE D 824 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG D 889 " --> pdb=" O PRO D 885 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 835 through 838 Processing sheet with id=AA5, first strand: chain 'D' and resid 835 through 838 removed outlier: 3.584A pdb=" N TYR D 917 " --> pdb=" O GLY D 944 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY D 944 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 62 through 64 removed outlier: 6.528A pdb=" N LEU F 52 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 3 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE F 126 " --> pdb=" O ILE F 3 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU F 5 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE F 128 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU F 7 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N TYR F 208 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA F 170 " --> pdb=" O TYR F 208 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL F 210 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL F 172 " --> pdb=" O VAL F 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 134 through 136 removed outlier: 3.933A pdb=" N LEU F 134 " --> pdb=" O GLN F 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 230 through 238 removed outlier: 3.742A pdb=" N GLU F 328 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL F 377 " --> pdb=" O LEU F 329 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY F 366 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N CYS F 347 " --> pdb=" O THR F 312 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N THR F 312 " --> pdb=" O CYS F 347 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN F 349 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AB1, first strand: chain 'G' and resid 827 through 828 Processing sheet with id=AB2, first strand: chain 'G' and resid 876 through 881 Processing sheet with id=AB3, first strand: chain 'G' and resid 876 through 881 Processing sheet with id=AB4, first strand: chain 'H' and resid 62 through 63 Processing sheet with id=AB5, first strand: chain 'I' and resid 194 through 196 removed outlier: 5.889A pdb=" N VAL I 123 " --> pdb=" O GLN I 195 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS I 2 " --> pdb=" O LYS I 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 68 through 71 Processing sheet with id=AB7, first strand: chain 'I' and resid 203 through 205 removed outlier: 5.823A pdb=" N SER I 223 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N SER I 238 " --> pdb=" O SER I 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 373 through 376 removed outlier: 6.869A pdb=" N TYR I 327 " --> pdb=" O PHE I 394 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL I 295 " --> pdb=" O VAL I 393 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU I 296 " --> pdb=" O ILE I 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 513 through 517 removed outlier: 5.042A pdb=" N HIS I 551 " --> pdb=" O LYS I 515 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY K 481 " --> pdb=" O VAL I 540 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LEU K 492 " --> pdb=" O PRO K 453 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY K 455 " --> pdb=" O LEU K 492 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE K 456 " --> pdb=" O GLU I 514 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 529 through 532 removed outlier: 7.317A pdb=" N ILE I 535 " --> pdb=" O ILE I 531 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 606 through 610 removed outlier: 6.268A pdb=" N THR I 633 " --> pdb=" O ARG K 510 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR K 512 " --> pdb=" O THR I 633 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE I 635 " --> pdb=" O THR K 512 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ARG K 514 " --> pdb=" O ILE I 635 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N CYS I 637 " --> pdb=" O ARG K 514 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N HIS K 516 " --> pdb=" O CYS I 637 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 133 through 136 removed outlier: 6.020A pdb=" N ILE K 90 " --> pdb=" O VAL K 134 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL K 136 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N MET K 92 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL K 64 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N THR K 93 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASN K 28 " --> pdb=" O CYS K 63 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ILE K 65 " --> pdb=" O ASN K 28 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET K 30 " --> pdb=" O ILE K 65 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 142 through 143 removed outlier: 3.609A pdb=" N LEU K 199 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 305 through 307 removed outlier: 6.741A pdb=" N TYR K 266 " --> pdb=" O PHE K 322 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS K 234 " --> pdb=" O MET K 347 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ILE K 349 " --> pdb=" O LYS K 234 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU K 236 " --> pdb=" O ILE K 349 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 369 through 370 removed outlier: 3.774A pdb=" N LEU K 378 " --> pdb=" O LEU K 370 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 45 through 48 removed outlier: 3.936A pdb=" N LEU Q 158 " --> pdb=" O GLN Q 46 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE Q 164 " --> pdb=" O SER Q 238 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL Q 237 " --> pdb=" O VAL Q 257 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE Q 259 " --> pdb=" O VAL Q 237 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG Q 239 " --> pdb=" O ILE Q 259 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Q' and resid 52 through 55 removed outlier: 3.691A pdb=" N GLU Q 277 " --> pdb=" O SER Q 285 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '1' and resid 1448 through 1449 removed outlier: 4.126A pdb=" N ARG 1 20 " --> pdb=" O MET 21172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '1' and resid 86 through 94 removed outlier: 10.174A pdb=" N LEU 1 90 " --> pdb=" O PRO 1 254 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N LYS 1 92 " --> pdb=" O VAL 1 252 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL 1 252 " --> pdb=" O LYS 1 92 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '1' and resid 190 through 194 Processing sheet with id=AD3, first strand: chain '1' and resid 357 through 359 removed outlier: 3.794A pdb=" N LYS 1 357 " --> pdb=" O PHE 21086 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '1' and resid 362 through 369 removed outlier: 7.698A pdb=" N PHE 1 482 " --> pdb=" O ARG 1 364 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL 1 366 " --> pdb=" O PHE 1 482 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU 1 484 " --> pdb=" O VAL 1 366 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR 1 368 " --> pdb=" O LEU 1 484 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET 1 470 " --> pdb=" O PHE 1 458 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR 1 365 " --> pdb=" O MET 1 501 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '1' and resid 390 through 393 removed outlier: 3.774A pdb=" N TYR 1 418 " --> pdb=" O GLU 1 447 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '1' and resid 579 through 581 removed outlier: 5.617A pdb=" N ILE 1 579 " --> pdb=" O TYR 6 93 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR 6 93 " --> pdb=" O ILE 1 579 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS 1 581 " --> pdb=" O VAL 6 91 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY 6 94 " --> pdb=" O VAL 6 141 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL 6 141 " --> pdb=" O GLY 6 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '1' and resid 579 through 581 removed outlier: 5.617A pdb=" N ILE 1 579 " --> pdb=" O TYR 6 93 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR 6 93 " --> pdb=" O ILE 1 579 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS 1 581 " --> pdb=" O VAL 6 91 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR 6 115 " --> pdb=" O TYR 6 97 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE 6 99 " --> pdb=" O SER 6 113 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER 6 113 " --> pdb=" O ILE 6 99 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY 6 101 " --> pdb=" O ARG 6 111 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG 6 111 " --> pdb=" O GLY 6 101 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LEU 6 122 " --> pdb=" O ASP 6 42 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP 6 42 " --> pdb=" O LEU 6 122 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU 6 31 " --> pdb=" O VAL 6 12 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL 6 12 " --> pdb=" O GLU 6 31 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS 6 55 " --> pdb=" O LEU 6 148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '1' and resid 602 through 605 removed outlier: 6.886A pdb=" N VAL 1 629 " --> pdb=" O ILE 1 636 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '1' and resid 685 through 686 removed outlier: 4.353A pdb=" N HIS 1 685 " --> pdb=" O SER 2 784 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE 21042 " --> pdb=" O ILE 2 782 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '1' and resid 872 through 873 removed outlier: 3.838A pdb=" N GLN 1 888 " --> pdb=" O VAL 1 879 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '1' and resid 902 through 905 Processing sheet with id=AE3, first strand: chain '1' and resid 1307 through 1310 removed outlier: 3.678A pdb=" N THR 11358 " --> pdb=" O THR 11140 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '1' and resid 1243 through 1247 removed outlier: 5.150A pdb=" N ILE 11261 " --> pdb=" O TRP 11210 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N TRP 11210 " --> pdb=" O ILE 11261 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR 7 54 " --> pdb=" O ILE 11175 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N TYR 11177 " --> pdb=" O CYS 7 52 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS 7 52 " --> pdb=" O TYR 11177 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '1' and resid 1319 through 1322 removed outlier: 3.589A pdb=" N LYS 11319 " --> pdb=" O LEU 11331 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '1' and resid 1472 through 1475 Processing sheet with id=AE7, first strand: chain '2' and resid 65 through 67 removed outlier: 6.508A pdb=" N LEU 2 86 " --> pdb=" O THR 2 131 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N THR 2 131 " --> pdb=" O LEU 2 86 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N PHE 2 88 " --> pdb=" O THR 2 129 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR 2 129 " --> pdb=" O PHE 2 88 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN 2 90 " --> pdb=" O ASP 2 127 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY 2 150 " --> pdb=" O LEU 2 124 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL 2 126 " --> pdb=" O PHE 2 148 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N PHE 2 148 " --> pdb=" O VAL 2 126 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE 2 128 " --> pdb=" O LYS 2 146 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LYS 2 146 " --> pdb=" O ILE 2 128 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS 2 130 " --> pdb=" O HIS 2 144 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N HIS 2 144 " --> pdb=" O LYS 2 130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '2' and resid 185 through 186 Processing sheet with id=AE9, first strand: chain '2' and resid 391 through 394 removed outlier: 6.445A pdb=" N ALA 2 196 " --> pdb=" O ASN 2 486 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '2' and resid 205 through 209 removed outlier: 3.653A pdb=" N PHE 2 208 " --> pdb=" O THR 2 218 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR 2 218 " --> pdb=" O PHE 2 208 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR 2 217 " --> pdb=" O MET 2 239 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '2' and resid 531 through 532 Processing sheet with id=AF3, first strand: chain '2' and resid 531 through 532 Processing sheet with id=AF4, first strand: chain '2' and resid 551 through 552 removed outlier: 5.208A pdb=" N TRP 2 573 " --> pdb=" O VAL 2 569 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL 2 569 " --> pdb=" O TRP 2 573 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY 2 575 " --> pdb=" O ILE 2 567 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU 2 611 " --> pdb=" O ASP 2 606 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '2' and resid 749 through 751 removed outlier: 3.556A pdb=" N CYS 2 919 " --> pdb=" O GLU 2 816 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '2' and resid 749 through 751 removed outlier: 6.577A pdb=" N PHE 2 918 " --> pdb=" O VAL 2 909 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL 2 909 " --> pdb=" O PHE 2 918 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS 2 920 " --> pdb=" O VAL 2 907 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL 2 907 " --> pdb=" O LYS 2 920 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ARG 2 922 " --> pdb=" O ASP 2 905 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL 2 907 " --> pdb=" O LYS a 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET a 15 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE a 28 " --> pdb=" O MET a 15 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '2' and resid 776 through 777 Processing sheet with id=AF8, first strand: chain '2' and resid 944 through 949 removed outlier: 7.039A pdb=" N VAL 2 794 " --> pdb=" O GLY 2 946 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN 2 948 " --> pdb=" O VAL 2 794 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N MET 2 796 " --> pdb=" O GLN 2 948 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE 2 795 " --> pdb=" O ILE 2 966 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain '2' and resid 827 through 829 Processing sheet with id=AG1, first strand: chain '2' and resid 956 through 957 Processing sheet with id=AG2, first strand: chain '2' and resid 1115 through 1119 Processing sheet with id=AG3, first strand: chain '2' and resid 1127 through 1129 Processing sheet with id=AG4, first strand: chain '3' and resid 8 through 14 removed outlier: 7.284A pdb=" N LYS 3 20 " --> pdb=" O THR 3 12 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU 3 14 " --> pdb=" O ASN 3 18 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN 3 18 " --> pdb=" O LEU 3 14 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '3' and resid 121 through 122 removed outlier: 6.751A pdb=" N GLU 3 158 " --> pdb=" O ASN 3 55 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASN 3 55 " --> pdb=" O GLU 3 158 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ARG 3 160 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LYS 3 166 " --> pdb=" O ILE 3 47 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE 3 47 " --> pdb=" O LYS 3 166 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY 3 168 " --> pdb=" O ILE 3 45 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE 3 45 " --> pdb=" O GLY 3 168 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '3' and resid 113 through 116 Processing sheet with id=AG7, first strand: chain '4' and resid 61 through 63 removed outlier: 6.066A pdb=" N GLN 4 71 " --> pdb=" O ARG 4 101 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU 4 103 " --> pdb=" O GLN 4 71 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE 4 73 " --> pdb=" O LEU 4 103 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL 4 105 " --> pdb=" O PHE 4 73 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE 4 75 " --> pdb=" O VAL 4 105 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA 4 102 " --> pdb=" O GLU 4 128 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N PHE 4 130 " --> pdb=" O ALA 4 102 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE 4 104 " --> pdb=" O PHE 4 130 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '4' and resid 147 through 150 removed outlier: 4.136A pdb=" N GLN 4 189 " --> pdb=" O VAL 4 209 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '5' and resid 56 through 57 removed outlier: 6.555A pdb=" N ILE 5 124 " --> pdb=" O MET 5 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain '7' and resid 16 through 17 Processing sheet with id=AH2, first strand: chain '7' and resid 25 through 29 removed outlier: 3.619A pdb=" N ILE 7 34 " --> pdb=" O ASP 7 29 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '7' and resid 94 through 97 Processing sheet with id=AH4, first strand: chain '9' and resid 19 through 23 Processing sheet with id=AH5, first strand: chain 'i' and resid 22 through 24 removed outlier: 3.560A pdb=" N LYS i 23 " --> pdb=" O ARG i 14 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG i 14 " --> pdb=" O LYS i 23 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'i' and resid 56 through 61 removed outlier: 6.988A pdb=" N PHE i 57 " --> pdb=" O VAL i 89 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL i 89 " --> pdb=" O PHE i 57 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLY i 59 " --> pdb=" O VAL i 87 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'j' and resid 214 through 216 removed outlier: 3.711A pdb=" N SER j 214 " --> pdb=" O GLU j 228 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN j 253 " --> pdb=" O THR j 181 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'j' and resid 278 through 280 removed outlier: 5.748A pdb=" N VAL j 293 " --> pdb=" O LYS j 306 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS j 306 " --> pdb=" O VAL j 293 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'j' and resid 352 through 355 Processing sheet with id=AI1, first strand: chain 'j' and resid 437 through 439 Processing sheet with id=AI2, first strand: chain 'j' and resid 510 through 513 removed outlier: 6.848A pdb=" N ILE j 501 " --> pdb=" O VAL j 493 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'j' and resid 567 through 571 removed outlier: 6.854A pdb=" N THR j 557 " --> pdb=" O LEU j 553 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU j 553 " --> pdb=" O THR j 557 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN j 559 " --> pdb=" O VAL j 551 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR j 576 " --> pdb=" O GLN j 541 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'j' and resid 635 through 639 removed outlier: 6.660A pdb=" N PHE j 621 " --> pdb=" O LEU j 617 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU j 617 " --> pdb=" O PHE j 621 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE j 623 " --> pdb=" O ARG j 615 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'j' and resid 742 through 746 removed outlier: 7.172A pdb=" N THR j 731 " --> pdb=" O ALA j 727 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA j 727 " --> pdb=" O THR j 731 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG j 733 " --> pdb=" O LYS j 725 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'k' and resid 38 through 39 removed outlier: 5.501A pdb=" N VAL k 45 " --> pdb=" O PHE k 77 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE k 77 " --> pdb=" O VAL k 45 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS k 73 " --> pdb=" O THR k 49 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE k 51 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS k 71 " --> pdb=" O ILE k 51 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN k 53 " --> pdb=" O PRO k 69 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'k' and resid 38 through 39 removed outlier: 5.501A pdb=" N VAL k 45 " --> pdb=" O PHE k 77 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE k 77 " --> pdb=" O VAL k 45 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS k 73 " --> pdb=" O THR k 49 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE k 51 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS k 71 " --> pdb=" O ILE k 51 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN k 53 " --> pdb=" O PRO k 69 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL k 70 " --> pdb=" O HIS k 9 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'k' and resid 169 through 170 removed outlier: 6.766A pdb=" N ILE k 160 " --> pdb=" O VAL k 148 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR k 150 " --> pdb=" O PHE k 158 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE k 158 " --> pdb=" O THR k 150 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER k 105 " --> pdb=" O ILE k 157 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA k 159 " --> pdb=" O SER k 105 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER k 109 " --> pdb=" O GLY k 161 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY k 96 " --> pdb=" O VAL k 92 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL k 92 " --> pdb=" O GLY k 96 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE k 98 " --> pdb=" O THR k 90 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'k' and resid 118 through 119 6221 hydrogen bonds defined for protein. 17949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 59.90 Time building geometry restraints manager: 36.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 28435 1.33 - 1.46: 26763 1.46 - 1.58: 58960 1.58 - 1.71: 204 1.71 - 1.83: 994 Bond restraints: 115356 Sorted by residual: bond pdb=" CA CYS B 582 " pdb=" C CYS B 582 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.38e-02 5.25e+03 1.74e+01 bond pdb=" N SER 11770 " pdb=" CA SER 11770 " ideal model delta sigma weight residual 1.462 1.491 -0.029 7.70e-03 1.69e+04 1.37e+01 bond pdb=" N ARG G 845 " pdb=" CA ARG G 845 " ideal model delta sigma weight residual 1.456 1.499 -0.042 1.21e-02 6.83e+03 1.22e+01 bond pdb=" N SER 11798 " pdb=" CA SER 11798 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.08e+01 bond pdb=" N ARG P 498 " pdb=" CA ARG P 498 " ideal model delta sigma weight residual 1.458 1.500 -0.043 1.33e-02 5.65e+03 1.04e+01 ... (remaining 115351 not shown) Histogram of bond angle deviations from ideal: 95.81 - 103.48: 1691 103.48 - 111.15: 48655 111.15 - 118.83: 45175 118.83 - 126.50: 59441 126.50 - 134.17: 1756 Bond angle restraints: 156718 Sorted by residual: angle pdb=" N PRO g 76 " pdb=" CA PRO g 76 " pdb=" CB PRO g 76 " ideal model delta sigma weight residual 102.81 109.33 -6.52 6.70e-01 2.23e+00 9.46e+01 angle pdb=" CA ASP G 275 " pdb=" CB ASP G 275 " pdb=" CG ASP G 275 " ideal model delta sigma weight residual 112.60 120.56 -7.96 1.00e+00 1.00e+00 6.33e+01 angle pdb=" N PRO h 5 " pdb=" CA PRO h 5 " pdb=" CB PRO h 5 " ideal model delta sigma weight residual 103.08 110.04 -6.96 9.70e-01 1.06e+00 5.16e+01 angle pdb=" N PRO g 60 " pdb=" CA PRO g 60 " pdb=" CB PRO g 60 " ideal model delta sigma weight residual 103.33 110.14 -6.81 1.10e+00 8.26e-01 3.83e+01 angle pdb=" O3' G c 38 " pdb=" C3' G c 38 " pdb=" C2' G c 38 " ideal model delta sigma weight residual 113.70 122.90 -9.20 1.50e+00 4.44e-01 3.76e+01 ... (remaining 156713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.47: 67757 33.47 - 66.94: 1537 66.94 - 100.41: 133 100.41 - 133.88: 3 133.88 - 167.35: 1 Dihedral angle restraints: 69431 sinusoidal: 27330 harmonic: 42101 Sorted by residual: dihedral pdb=" C4' G c 34 " pdb=" C3' G c 34 " pdb=" C2' G c 34 " pdb=" C1' G c 34 " ideal model delta sinusoidal sigma weight residual 36.00 -44.48 80.48 1 8.00e+00 1.56e-02 1.25e+02 dihedral pdb=" O4' G c 34 " pdb=" C2' G c 34 " pdb=" C1' G c 34 " pdb=" C3' G c 34 " ideal model delta sinusoidal sigma weight residual 25.00 -48.25 73.25 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" C4' C c 29 " pdb=" C3' C c 29 " pdb=" C2' C c 29 " pdb=" C1' C c 29 " ideal model delta sinusoidal sigma weight residual 36.00 -35.11 71.11 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 69428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 15510 0.059 - 0.117: 2173 0.117 - 0.176: 218 0.176 - 0.235: 20 0.235 - 0.293: 3 Chirality restraints: 17924 Sorted by residual: chirality pdb=" P G c 32 " pdb=" OP1 G c 32 " pdb=" OP2 G c 32 " pdb=" O5' G c 32 " both_signs ideal model delta sigma weight residual True 2.41 -2.70 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" P G c 38 " pdb=" OP1 G c 38 " pdb=" OP2 G c 38 " pdb=" O5' G c 38 " both_signs ideal model delta sigma weight residual True 2.41 -2.69 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' G c 34 " pdb=" C4' G c 34 " pdb=" O3' G c 34 " pdb=" C2' G c 34 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 17921 not shown) Planarity restraints: 20059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG P 498 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ARG P 498 " 0.055 2.00e-02 2.50e+03 pdb=" O ARG P 498 " -0.020 2.00e-02 2.50e+03 pdb=" N MET P 499 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP i 70 " 0.022 2.00e-02 2.50e+03 1.86e-02 8.68e+00 pdb=" CG TRP i 70 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP i 70 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP i 70 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP i 70 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP i 70 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP i 70 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP i 70 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP i 70 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP i 70 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR 2 678 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO 2 679 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO 2 679 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO 2 679 " -0.036 5.00e-02 4.00e+02 ... (remaining 20056 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 292 2.36 - 2.99: 68784 2.99 - 3.63: 179461 3.63 - 4.26: 253148 4.26 - 4.90: 414766 Nonbonded interactions: 916451 Sorted by model distance: nonbonded pdb=" OD1 ASN Q 117 " pdb="MN MN Q 501 " model vdw 1.722 2.320 nonbonded pdb=" NE2 HIS Q 167 " pdb="MN MN Q 501 " model vdw 1.768 2.400 nonbonded pdb=" OD2 ASP 1 499 " pdb="MG MG 12101 " model vdw 1.902 2.170 nonbonded pdb=" OD1 ASP 1 499 " pdb="MG MG 12101 " model vdw 1.942 2.170 nonbonded pdb=" OD2 ASP Q 85 " pdb="MN MN Q 501 " model vdw 1.975 2.320 ... (remaining 916446 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 17.630 Check model and map are aligned: 1.210 Set scattering table: 0.750 Process input model: 255.750 Find NCS groups from input model: 3.670 Set up NCS constraints: 0.320 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 285.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 0.060 115356 Z= 0.264 Angle : 0.634 10.567 156718 Z= 0.375 Chirality : 0.041 0.293 17924 Planarity : 0.004 0.072 20059 Dihedral : 14.150 167.352 42345 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.53 % Favored : 94.32 % Rotamer: Outliers : 0.18 % Allowed : 0.45 % Favored : 99.37 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.17 % 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: 0.51 (0.07), residues: 14510 helix: 1.56 (0.06), residues: 7857 sheet: -0.58 (0.16), residues: 1146 loop : -1.27 (0.08), residues: 5507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP i 70 HIS 0.013 0.001 HIS D 900 PHE 0.038 0.001 PHE D 948 TYR 0.025 0.001 TYR I 182 ARG 0.014 0.001 ARG 1 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1057 time to evaluate : 9.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 791 MET cc_start: 0.7679 (ttt) cc_final: 0.7232 (mtt) REVERT: A 1286 MET cc_start: 0.9002 (mpp) cc_final: 0.8614 (mpp) REVERT: A 1883 MET cc_start: 0.8479 (tmm) cc_final: 0.8252 (tmm) REVERT: A 2051 MET cc_start: 0.8328 (pmm) cc_final: 0.7953 (tmm) REVERT: B 350 ILE cc_start: 0.8678 (mm) cc_final: 0.8238 (mm) REVERT: B 396 MET cc_start: 0.8892 (mpp) cc_final: 0.8687 (mpp) REVERT: B 1065 CYS cc_start: 0.8100 (m) cc_final: 0.7774 (m) REVERT: D 173 LEU cc_start: 0.9091 (tp) cc_final: 0.8887 (tp) REVERT: D 874 MET cc_start: 0.8783 (tpp) cc_final: 0.8557 (tpp) REVERT: E 972 ASP cc_start: 0.7661 (t0) cc_final: 0.7447 (t0) REVERT: F 74 MET cc_start: 0.7098 (mmm) cc_final: 0.6707 (mmt) REVERT: F 382 MET cc_start: 0.7648 (mpp) cc_final: 0.7412 (mpp) REVERT: F 438 ASN cc_start: 0.8968 (m-40) cc_final: 0.8765 (m-40) REVERT: G 27 MET cc_start: 0.8023 (ptm) cc_final: 0.7654 (ttp) REVERT: G 246 LEU cc_start: 0.8884 (pt) cc_final: 0.8672 (pp) REVERT: G 275 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8058 (t0) REVERT: G 536 MET cc_start: 0.7878 (mmm) cc_final: 0.7559 (mmm) REVERT: G 681 LEU cc_start: 0.9443 (tp) cc_final: 0.9189 (tt) REVERT: G 696 ASP cc_start: 0.7667 (p0) cc_final: 0.7449 (p0) REVERT: G 873 MET cc_start: 0.5577 (mmt) cc_final: 0.5363 (mpp) REVERT: H 329 VAL cc_start: 0.9257 (t) cc_final: 0.8988 (p) REVERT: H 535 MET cc_start: 0.8613 (ppp) cc_final: 0.8311 (ppp) REVERT: H 648 MET cc_start: 0.8444 (ppp) cc_final: 0.7815 (ppp) REVERT: H 884 MET cc_start: 0.8496 (mmp) cc_final: 0.8250 (mmp) REVERT: I 108 MET cc_start: 0.8582 (tpp) cc_final: 0.8174 (tpp) REVERT: I 137 MET cc_start: 0.8625 (mtm) cc_final: 0.8099 (mtm) REVERT: P 528 MET cc_start: 0.8424 (mtp) cc_final: 0.7920 (ttm) REVERT: Q 64 ASP cc_start: 0.7649 (m-30) cc_final: 0.7279 (m-30) REVERT: 1 329 MET cc_start: 0.5697 (ppp) cc_final: 0.5413 (ppp) REVERT: 1 660 MET cc_start: 0.8560 (mpp) cc_final: 0.8206 (mpp) REVERT: 1 1309 MET cc_start: 0.8104 (pmm) cc_final: 0.7684 (pmm) REVERT: 2 30 ILE cc_start: 0.9180 (mt) cc_final: 0.8882 (tp) REVERT: 2 155 MET cc_start: 0.7518 (ptp) cc_final: 0.7163 (ptp) REVERT: 2 594 MET cc_start: 0.8704 (pmm) cc_final: 0.8288 (pmm) REVERT: 2 1054 MET cc_start: 0.8184 (tpt) cc_final: 0.7965 (tpt) REVERT: 2 1092 ASP cc_start: 0.7814 (m-30) cc_final: 0.7169 (m-30) REVERT: 6 9 ILE cc_start: 0.8812 (mm) cc_final: 0.8513 (mm) REVERT: 6 41 LEU cc_start: 0.8036 (tp) cc_final: 0.7636 (tp) REVERT: 9 44 ASN cc_start: 0.7883 (t0) cc_final: 0.7636 (p0) REVERT: 9 102 GLU cc_start: 0.7852 (tt0) cc_final: 0.7618 (tt0) REVERT: g 585 ASN cc_start: 0.7403 (m-40) cc_final: 0.6599 (t0) REVERT: j 451 MET cc_start: 0.8508 (mmp) cc_final: 0.8110 (mmp) REVERT: k 156 ASP cc_start: 0.7291 (m-30) cc_final: 0.6682 (t0) outliers start: 21 outliers final: 6 residues processed: 1074 average time/residue: 0.8947 time to fit residues: 1714.1662 Evaluate side-chains 759 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 752 time to evaluate : 9.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1469 random chunks: chunk 1240 optimal weight: 6.9990 chunk 1113 optimal weight: 0.6980 chunk 617 optimal weight: 0.9990 chunk 380 optimal weight: 50.0000 chunk 751 optimal weight: 3.9990 chunk 594 optimal weight: 6.9990 chunk 1151 optimal weight: 5.9990 chunk 445 optimal weight: 3.9990 chunk 700 optimal weight: 0.9980 chunk 856 optimal weight: 0.8980 chunk 1334 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 HIS D 492 ASN D 553 ASN D 908 GLN E 888 HIS E 903 HIS E 984 HIS F 225 GLN ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 451 HIS H 879 GLN ** H 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 GLN 1 123 ASN 1 432 HIS 1 441 GLN 1 531 ASN 1 620 HIS 1 746 ASN 11457 ASN 11462 GLN 2 111 ASN 2 197 GLN ** 2 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 265 HIS 3 268 GLN 4 132 GLN 9 113 GLN ** e 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 HIS l 47 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 115356 Z= 0.188 Angle : 0.570 10.775 156718 Z= 0.294 Chirality : 0.041 0.321 17924 Planarity : 0.004 0.065 20059 Dihedral : 9.579 165.750 16886 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.51 % Favored : 95.35 % Rotamer: Outliers : 0.10 % Allowed : 3.96 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.88 (0.07), residues: 14510 helix: 1.80 (0.06), residues: 7874 sheet: -0.45 (0.15), residues: 1168 loop : -0.99 (0.09), residues: 5468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP i 70 HIS 0.016 0.001 HIS B1002 PHE 0.034 0.002 PHE g 240 TYR 0.017 0.001 TYR 11797 ARG 0.008 0.000 ARG k 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1076 time to evaluate : 9.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 791 MET cc_start: 0.7698 (ttt) cc_final: 0.7221 (mtt) REVERT: A 1864 MET cc_start: 0.7652 (mmt) cc_final: 0.7435 (mmm) REVERT: A 1883 MET cc_start: 0.7994 (tmm) cc_final: 0.7631 (tmm) REVERT: A 2051 MET cc_start: 0.8517 (pmm) cc_final: 0.8125 (tmm) REVERT: B 211 LEU cc_start: 0.9358 (pp) cc_final: 0.9137 (tp) REVERT: B 212 CYS cc_start: 0.8423 (m) cc_final: 0.7932 (p) REVERT: B 339 MET cc_start: 0.8722 (ppp) cc_final: 0.8237 (ppp) REVERT: B 343 LEU cc_start: 0.9039 (mt) cc_final: 0.8606 (mt) REVERT: B 684 MET cc_start: 0.8536 (mmm) cc_final: 0.8283 (mmm) REVERT: B 1065 CYS cc_start: 0.8212 (m) cc_final: 0.7931 (m) REVERT: B 1091 LEU cc_start: 0.8653 (tp) cc_final: 0.8240 (tp) REVERT: D 211 VAL cc_start: 0.9080 (t) cc_final: 0.8808 (p) REVERT: D 290 MET cc_start: 0.8802 (tmm) cc_final: 0.8349 (tmm) REVERT: D 424 ILE cc_start: 0.9073 (mm) cc_final: 0.8846 (mm) REVERT: D 787 LEU cc_start: 0.8978 (mt) cc_final: 0.8749 (mt) REVERT: D 848 ASP cc_start: 0.8043 (m-30) cc_final: 0.7279 (m-30) REVERT: E 972 ASP cc_start: 0.7631 (t0) cc_final: 0.7396 (t0) REVERT: F 52 LEU cc_start: 0.8530 (tp) cc_final: 0.8278 (tp) REVERT: F 559 MET cc_start: 0.7461 (mtp) cc_final: 0.7256 (mtt) REVERT: G 246 LEU cc_start: 0.8959 (pt) cc_final: 0.8692 (pp) REVERT: G 536 MET cc_start: 0.7809 (mmm) cc_final: 0.7572 (mmm) REVERT: G 696 ASP cc_start: 0.7553 (p0) cc_final: 0.7344 (p0) REVERT: H 329 VAL cc_start: 0.9181 (t) cc_final: 0.8916 (p) REVERT: H 535 MET cc_start: 0.8354 (ppp) cc_final: 0.7984 (ppp) REVERT: H 648 MET cc_start: 0.8545 (ppp) cc_final: 0.8020 (ppp) REVERT: H 752 MET cc_start: 0.5326 (mmt) cc_final: 0.5083 (mmt) REVERT: I 32 MET cc_start: 0.8757 (tpp) cc_final: 0.8535 (tpp) REVERT: I 137 MET cc_start: 0.8459 (mtm) cc_final: 0.8250 (mtm) REVERT: I 250 MET cc_start: 0.8111 (tmm) cc_final: 0.7686 (tmm) REVERT: K 299 MET cc_start: 0.7831 (mmm) cc_final: 0.7604 (mmm) REVERT: K 420 MET cc_start: 0.7667 (mmt) cc_final: 0.6923 (mtp) REVERT: Q 223 ASP cc_start: 0.8282 (p0) cc_final: 0.7695 (p0) REVERT: 1 238 MET cc_start: 0.7465 (ppp) cc_final: 0.6998 (ppp) REVERT: 1 329 MET cc_start: 0.6088 (ppp) cc_final: 0.5850 (ppp) REVERT: 1 467 MET cc_start: 0.7667 (mtp) cc_final: 0.7128 (mtp) REVERT: 1 501 MET cc_start: 0.8767 (ttm) cc_final: 0.8353 (ttm) REVERT: 1 592 PHE cc_start: 0.8018 (t80) cc_final: 0.7812 (t80) REVERT: 1 637 MET cc_start: 0.7680 (ppp) cc_final: 0.6923 (ppp) REVERT: 1 660 MET cc_start: 0.8499 (mpp) cc_final: 0.8299 (mpp) REVERT: 1 1309 MET cc_start: 0.8178 (pmm) cc_final: 0.7832 (pmm) REVERT: 2 155 MET cc_start: 0.7569 (ptp) cc_final: 0.7172 (ptp) REVERT: 2 298 MET cc_start: 0.8193 (ttp) cc_final: 0.7991 (ttt) REVERT: 2 365 LEU cc_start: 0.9603 (mt) cc_final: 0.9399 (mt) REVERT: 2 529 MET cc_start: 0.7891 (mmm) cc_final: 0.7556 (mmm) REVERT: 2 594 MET cc_start: 0.8630 (pmm) cc_final: 0.8291 (pmm) REVERT: 2 1054 MET cc_start: 0.8174 (tpt) cc_final: 0.7891 (mmm) REVERT: 6 9 ILE cc_start: 0.8491 (mm) cc_final: 0.8278 (mm) REVERT: 6 92 MET cc_start: 0.4866 (mtt) cc_final: 0.4523 (mtt) REVERT: 8 55 LEU cc_start: 0.8883 (mp) cc_final: 0.8678 (mp) REVERT: 9 102 GLU cc_start: 0.7772 (tt0) cc_final: 0.7533 (tt0) REVERT: g 425 MET cc_start: 0.8219 (tmm) cc_final: 0.7796 (ptp) REVERT: g 585 ASN cc_start: 0.7471 (m-40) cc_final: 0.6727 (t0) outliers start: 11 outliers final: 2 residues processed: 1085 average time/residue: 0.8758 time to fit residues: 1700.3599 Evaluate side-chains 799 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 797 time to evaluate : 9.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1469 random chunks: chunk 741 optimal weight: 6.9990 chunk 414 optimal weight: 6.9990 chunk 1110 optimal weight: 8.9990 chunk 908 optimal weight: 6.9990 chunk 367 optimal weight: 9.9990 chunk 1336 optimal weight: 40.0000 chunk 1443 optimal weight: 5.9990 chunk 1190 optimal weight: 6.9990 chunk 1325 optimal weight: 9.9990 chunk 455 optimal weight: 6.9990 chunk 1072 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1666 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 232 ASN ** B 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 GLN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 ASN B 901 GLN B1036 HIS ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 492 ASN D 644 GLN ** D 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 864 GLN E 888 HIS F 90 GLN ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 HIS ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 902 HIS H 273 ASN ** H 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN ** K 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 232 ASN 1 278 HIS 1 441 GLN ** 1 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 700 GLN 1 704 ASN 1 746 ASN 1 790 GLN 1 904 GLN ** 11093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11101 GLN 11299 GLN 11445 HIS 11462 GLN 2 390 ASN ** 2 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 906 GLN ** 2 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 21117 HIS 4 169 GLN ** 6 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 52 HIS ** e 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 489 GLN ** i 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 509 HIS j 519 GLN j 625 HIS l 102 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 115356 Z= 0.473 Angle : 0.745 15.303 156718 Z= 0.381 Chirality : 0.045 0.296 17924 Planarity : 0.005 0.090 20059 Dihedral : 9.770 167.032 16886 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.02 % Favored : 93.84 % Rotamer: Outliers : 0.14 % Allowed : 6.35 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.14 % 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: 0.41 (0.07), residues: 14510 helix: 1.42 (0.06), residues: 7895 sheet: -0.63 (0.15), residues: 1196 loop : -1.24 (0.08), residues: 5419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP j 180 HIS 0.022 0.002 HIS D 568 PHE 0.046 0.002 PHE 9 87 TYR 0.045 0.002 TYR 11797 ARG 0.017 0.001 ARG Q 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 941 time to evaluate : 9.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 MET cc_start: 0.8069 (mmt) cc_final: 0.7776 (mmp) REVERT: A 767 MET cc_start: 0.9309 (pmm) cc_final: 0.9075 (pmm) REVERT: A 791 MET cc_start: 0.7877 (ttt) cc_final: 0.7370 (mtt) REVERT: A 1883 MET cc_start: 0.8266 (tmm) cc_final: 0.7690 (tmm) REVERT: B 211 LEU cc_start: 0.9438 (pp) cc_final: 0.9209 (tp) REVERT: B 343 LEU cc_start: 0.9125 (mt) cc_final: 0.8919 (mt) REVERT: B 480 LEU cc_start: 0.9325 (tp) cc_final: 0.9104 (pp) REVERT: B 684 MET cc_start: 0.8925 (mmm) cc_final: 0.8070 (tpp) REVERT: D 290 MET cc_start: 0.8947 (tmm) cc_final: 0.8729 (tmm) REVERT: E 972 ASP cc_start: 0.7758 (t0) cc_final: 0.7505 (t0) REVERT: F 52 LEU cc_start: 0.8702 (tp) cc_final: 0.8441 (tp) REVERT: F 379 LEU cc_start: 0.9090 (tp) cc_final: 0.8828 (pt) REVERT: G 246 LEU cc_start: 0.9118 (pt) cc_final: 0.8881 (pp) REVERT: G 536 MET cc_start: 0.7994 (mmm) cc_final: 0.7733 (mmm) REVERT: G 696 ASP cc_start: 0.7891 (p0) cc_final: 0.7517 (p0) REVERT: H 471 ASP cc_start: 0.8716 (p0) cc_final: 0.8516 (p0) REVERT: H 535 MET cc_start: 0.8455 (ppp) cc_final: 0.8178 (ppp) REVERT: H 648 MET cc_start: 0.8748 (ppp) cc_final: 0.8207 (ppp) REVERT: I 32 MET cc_start: 0.8581 (tpp) cc_final: 0.8367 (tpp) REVERT: I 107 MET cc_start: 0.9083 (ppp) cc_final: 0.8865 (ppp) REVERT: I 250 MET cc_start: 0.8113 (tmm) cc_final: 0.7864 (tmm) REVERT: K 35 MET cc_start: 0.7934 (ppp) cc_final: 0.7717 (ppp) REVERT: K 240 PHE cc_start: 0.7516 (p90) cc_final: 0.7261 (p90) REVERT: K 287 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8188 (p0) REVERT: K 299 MET cc_start: 0.8284 (mmm) cc_final: 0.7969 (mmm) REVERT: K 420 MET cc_start: 0.7960 (mmt) cc_final: 0.7582 (mtp) REVERT: P 499 MET cc_start: 0.8654 (mmm) cc_final: 0.8420 (mmp) REVERT: Q 17 LEU cc_start: 0.9563 (mt) cc_final: 0.9352 (mt) REVERT: Q 223 ASP cc_start: 0.8550 (p0) cc_final: 0.8000 (p0) REVERT: 1 78 MET cc_start: 0.8210 (mpp) cc_final: 0.7670 (mpp) REVERT: 1 653 VAL cc_start: 0.8174 (m) cc_final: 0.7738 (t) REVERT: 1 660 MET cc_start: 0.8621 (mpp) cc_final: 0.8331 (mpp) REVERT: 1 725 LEU cc_start: 0.8503 (tt) cc_final: 0.8295 (mp) REVERT: 1 1309 MET cc_start: 0.8056 (pmm) cc_final: 0.7658 (pmm) REVERT: 2 508 MET cc_start: 0.8467 (mpp) cc_final: 0.7917 (mpp) REVERT: 2 594 MET cc_start: 0.8763 (pmm) cc_final: 0.8350 (pmm) REVERT: 2 1054 MET cc_start: 0.8044 (tpt) cc_final: 0.7773 (tpt) REVERT: 2 1092 ASP cc_start: 0.7826 (m-30) cc_final: 0.7251 (m-30) REVERT: 3 234 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7767 (tt0) REVERT: 6 9 ILE cc_start: 0.8737 (mm) cc_final: 0.8514 (mm) REVERT: 7 49 ASP cc_start: 0.9116 (p0) cc_final: 0.8823 (p0) REVERT: 9 44 ASN cc_start: 0.7976 (t0) cc_final: 0.7669 (p0) REVERT: g 425 MET cc_start: 0.8218 (tmm) cc_final: 0.7583 (ptp) REVERT: g 585 ASN cc_start: 0.7498 (m-40) cc_final: 0.6690 (t0) outliers start: 16 outliers final: 5 residues processed: 954 average time/residue: 0.9002 time to fit residues: 1534.9098 Evaluate side-chains 748 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 742 time to evaluate : 9.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1469 random chunks: chunk 1320 optimal weight: 30.0000 chunk 1004 optimal weight: 3.9990 chunk 693 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 637 optimal weight: 7.9990 chunk 897 optimal weight: 6.9990 chunk 1341 optimal weight: 8.9990 chunk 1419 optimal weight: 5.9990 chunk 700 optimal weight: 4.9990 chunk 1271 optimal weight: 7.9990 chunk 382 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 ASN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 ASN ** D 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 HIS ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 612 ASN G 670 GLN ** G 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN ** P 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 441 GLN ** 1 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 746 ASN 11462 GLN ** 2 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 265 HIS ** 6 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 115356 Z= 0.342 Angle : 0.641 14.291 156718 Z= 0.329 Chirality : 0.043 0.235 17924 Planarity : 0.004 0.058 20059 Dihedral : 9.726 166.580 16886 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.32 % Favored : 94.56 % Rotamer: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.14 % 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: 0.51 (0.07), residues: 14510 helix: 1.50 (0.06), residues: 7896 sheet: -0.51 (0.15), residues: 1184 loop : -1.21 (0.08), residues: 5430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 3 176 HIS 0.015 0.001 HIS G 140 PHE 0.042 0.002 PHE 9 87 TYR 0.026 0.002 TYR 11797 ARG 0.010 0.000 ARG 2 721 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 965 time to evaluate : 8.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 MET cc_start: 0.7970 (mmt) cc_final: 0.7723 (mmp) REVERT: A 765 MET cc_start: 0.8892 (ptp) cc_final: 0.8330 (ptp) REVERT: A 791 MET cc_start: 0.7905 (ttt) cc_final: 0.7392 (mtt) REVERT: A 1864 MET cc_start: 0.8132 (mmt) cc_final: 0.7874 (mmm) REVERT: A 1883 MET cc_start: 0.8180 (tmm) cc_final: 0.7667 (tmm) REVERT: A 2047 MET cc_start: 0.8683 (ptp) cc_final: 0.8469 (ptp) REVERT: A 2051 MET cc_start: 0.8449 (pmm) cc_final: 0.7781 (tmm) REVERT: B 52 MET cc_start: 0.8222 (mmt) cc_final: 0.7969 (mmt) REVERT: B 210 PHE cc_start: 0.8336 (m-10) cc_final: 0.8127 (m-80) REVERT: B 211 LEU cc_start: 0.9373 (pp) cc_final: 0.9151 (tp) REVERT: B 455 TRP cc_start: 0.8161 (t60) cc_final: 0.7741 (t60) REVERT: B 483 VAL cc_start: 0.9544 (t) cc_final: 0.9223 (p) REVERT: B 684 MET cc_start: 0.8826 (mmm) cc_final: 0.8076 (tpp) REVERT: D 826 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7249 (mt-10) REVERT: D 848 ASP cc_start: 0.8077 (m-30) cc_final: 0.7312 (m-30) REVERT: E 639 LEU cc_start: 0.7860 (tp) cc_final: 0.7473 (pt) REVERT: E 972 ASP cc_start: 0.7691 (t0) cc_final: 0.7419 (t0) REVERT: F 52 LEU cc_start: 0.8571 (tp) cc_final: 0.8332 (tp) REVERT: F 379 LEU cc_start: 0.9127 (tp) cc_final: 0.8831 (pt) REVERT: F 559 MET cc_start: 0.7771 (mpp) cc_final: 0.7317 (mtm) REVERT: G 125 MET cc_start: 0.8427 (tpp) cc_final: 0.7903 (tpp) REVERT: G 246 LEU cc_start: 0.9052 (pt) cc_final: 0.8841 (pp) REVERT: G 536 MET cc_start: 0.7925 (mmm) cc_final: 0.7639 (mmm) REVERT: G 696 ASP cc_start: 0.7694 (p0) cc_final: 0.7327 (p0) REVERT: H 329 VAL cc_start: 0.9242 (t) cc_final: 0.8980 (p) REVERT: H 471 ASP cc_start: 0.8666 (p0) cc_final: 0.8459 (p0) REVERT: H 535 MET cc_start: 0.8484 (ppp) cc_final: 0.8163 (ppp) REVERT: H 648 MET cc_start: 0.8761 (ppp) cc_final: 0.8228 (ppp) REVERT: I 250 MET cc_start: 0.8088 (tmm) cc_final: 0.7802 (tmm) REVERT: K 149 GLU cc_start: 0.8626 (pm20) cc_final: 0.8394 (pm20) REVERT: K 240 PHE cc_start: 0.7512 (p90) cc_final: 0.7129 (p90) REVERT: K 299 MET cc_start: 0.8303 (mmm) cc_final: 0.7873 (mmm) REVERT: K 420 MET cc_start: 0.8092 (mmt) cc_final: 0.7709 (mtp) REVERT: Q 223 ASP cc_start: 0.8371 (p0) cc_final: 0.7834 (p0) REVERT: 1 467 MET cc_start: 0.7677 (mtp) cc_final: 0.7314 (mtp) REVERT: 1 660 MET cc_start: 0.8645 (mpp) cc_final: 0.8146 (mpp) REVERT: 1 1086 MET cc_start: 0.8585 (mmm) cc_final: 0.8103 (mmp) REVERT: 1 1309 MET cc_start: 0.8075 (pmm) cc_final: 0.7800 (pmm) REVERT: 2 155 MET cc_start: 0.7682 (ptp) cc_final: 0.7350 (ptp) REVERT: 2 513 GLU cc_start: 0.7503 (tt0) cc_final: 0.7138 (tt0) REVERT: 2 726 SER cc_start: 0.8650 (t) cc_final: 0.8327 (t) REVERT: 2 1094 GLN cc_start: 0.9089 (tp-100) cc_final: 0.8885 (tp40) REVERT: 6 92 MET cc_start: 0.6133 (mtt) cc_final: 0.5618 (mtt) REVERT: 7 49 ASP cc_start: 0.9059 (p0) cc_final: 0.8670 (p0) REVERT: a 31 ARG cc_start: 0.7252 (mtm180) cc_final: 0.7042 (mtm180) REVERT: g 425 MET cc_start: 0.8133 (tmm) cc_final: 0.7497 (ptp) REVERT: g 585 ASN cc_start: 0.7406 (m-40) cc_final: 0.6623 (t0) outliers start: 8 outliers final: 1 residues processed: 972 average time/residue: 0.8805 time to fit residues: 1531.1862 Evaluate side-chains 734 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 733 time to evaluate : 9.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1469 random chunks: chunk 1182 optimal weight: 20.0000 chunk 806 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 1057 optimal weight: 9.9990 chunk 585 optimal weight: 0.8980 chunk 1211 optimal weight: 20.0000 chunk 981 optimal weight: 2.9990 chunk 1 optimal weight: 40.0000 chunk 725 optimal weight: 0.0970 chunk 1274 optimal weight: 40.0000 chunk 358 optimal weight: 0.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS D 289 HIS D 492 ASN ** D 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 441 GLN ** 1 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 746 ASN 11462 GLN ** 2 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 GLN 9 49 GLN ** e 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 27 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 115356 Z= 0.179 Angle : 0.569 13.410 156718 Z= 0.290 Chirality : 0.041 0.194 17924 Planarity : 0.004 0.059 20059 Dihedral : 9.593 167.363 16886 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.98 % Favored : 94.90 % Rotamer: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.78 (0.07), residues: 14510 helix: 1.72 (0.06), residues: 7888 sheet: -0.43 (0.15), residues: 1203 loop : -1.07 (0.09), residues: 5419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 455 HIS 0.011 0.001 HIS 9 40 PHE 0.040 0.001 PHE 9 87 TYR 0.025 0.001 TYR 4 90 ARG 0.006 0.000 ARG Q 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1053 time to evaluate : 9.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 767 MET cc_start: 0.9312 (pmm) cc_final: 0.8916 (pmm) REVERT: A 791 MET cc_start: 0.7893 (ttt) cc_final: 0.7490 (mtt) REVERT: A 1883 MET cc_start: 0.8073 (tmm) cc_final: 0.7595 (tmm) REVERT: A 1887 LEU cc_start: 0.8011 (mt) cc_final: 0.7696 (mt) REVERT: A 2051 MET cc_start: 0.8446 (pmm) cc_final: 0.7839 (tmm) REVERT: B 211 LEU cc_start: 0.9338 (pp) cc_final: 0.9100 (tp) REVERT: B 435 MET cc_start: 0.7868 (tpp) cc_final: 0.7214 (tpp) REVERT: B 483 VAL cc_start: 0.9542 (t) cc_final: 0.9184 (p) REVERT: B 684 MET cc_start: 0.8766 (mmm) cc_final: 0.8007 (tpp) REVERT: B 1020 TYR cc_start: 0.8694 (p90) cc_final: 0.8394 (p90) REVERT: B 1065 CYS cc_start: 0.8177 (m) cc_final: 0.7934 (m) REVERT: D 848 ASP cc_start: 0.7967 (m-30) cc_final: 0.7062 (m-30) REVERT: D 874 MET cc_start: 0.8813 (tpp) cc_final: 0.8563 (tpp) REVERT: E 873 TYR cc_start: 0.8441 (m-80) cc_final: 0.8111 (m-80) REVERT: E 972 ASP cc_start: 0.7701 (t0) cc_final: 0.7449 (t0) REVERT: F 52 LEU cc_start: 0.8459 (tp) cc_final: 0.8211 (tp) REVERT: F 379 LEU cc_start: 0.9073 (tp) cc_final: 0.8799 (pt) REVERT: G 125 MET cc_start: 0.8381 (tpp) cc_final: 0.7723 (tpp) REVERT: G 536 MET cc_start: 0.7662 (mmm) cc_final: 0.7439 (mmm) REVERT: G 873 MET cc_start: 0.5417 (mpp) cc_final: 0.5185 (mpp) REVERT: G 893 LEU cc_start: 0.9225 (tp) cc_final: 0.8997 (tp) REVERT: H 329 VAL cc_start: 0.9193 (t) cc_final: 0.8931 (p) REVERT: H 471 ASP cc_start: 0.8695 (p0) cc_final: 0.8489 (p0) REVERT: H 535 MET cc_start: 0.8414 (ppp) cc_final: 0.8155 (ppp) REVERT: H 648 MET cc_start: 0.8720 (ppp) cc_final: 0.8201 (ppp) REVERT: I 107 MET cc_start: 0.8955 (ppp) cc_final: 0.8633 (tmm) REVERT: I 250 MET cc_start: 0.8121 (tmm) cc_final: 0.7721 (tmm) REVERT: K 240 PHE cc_start: 0.7273 (p90) cc_final: 0.6920 (p90) REVERT: K 299 MET cc_start: 0.8234 (mmm) cc_final: 0.7785 (mmm) REVERT: K 420 MET cc_start: 0.8097 (mmt) cc_final: 0.7882 (mtp) REVERT: Q 223 ASP cc_start: 0.8264 (p0) cc_final: 0.7613 (p0) REVERT: 1 78 MET cc_start: 0.7591 (mpp) cc_final: 0.7071 (mpp) REVERT: 1 637 MET cc_start: 0.7712 (ppp) cc_final: 0.6989 (ppp) REVERT: 1 660 MET cc_start: 0.8617 (mpp) cc_final: 0.8134 (mpp) REVERT: 1 1086 MET cc_start: 0.8540 (mmm) cc_final: 0.8095 (mmp) REVERT: 1 1309 MET cc_start: 0.7972 (pmm) cc_final: 0.7749 (pmm) REVERT: 2 155 MET cc_start: 0.7655 (ptp) cc_final: 0.7231 (ptp) REVERT: 2 513 GLU cc_start: 0.7330 (tt0) cc_final: 0.6922 (tt0) REVERT: 2 529 MET cc_start: 0.8032 (mmm) cc_final: 0.7617 (mmm) REVERT: 2 702 MET cc_start: 0.8164 (mmp) cc_final: 0.7855 (mmp) REVERT: 4 90 TYR cc_start: 0.8468 (m-80) cc_final: 0.8058 (m-80) REVERT: 6 24 ARG cc_start: 0.6072 (pmt-80) cc_final: 0.5085 (pmt170) REVERT: 6 92 MET cc_start: 0.5939 (mtt) cc_final: 0.5406 (mtt) REVERT: 7 49 ASP cc_start: 0.9055 (p0) cc_final: 0.8641 (p0) REVERT: 7 103 ARG cc_start: 0.7718 (ptt-90) cc_final: 0.7450 (ptt-90) REVERT: 9 49 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7300 (tp40) REVERT: g 425 MET cc_start: 0.7957 (tmm) cc_final: 0.7479 (ptp) REVERT: g 532 TYR cc_start: 0.7641 (t80) cc_final: 0.7430 (t80) REVERT: g 585 ASN cc_start: 0.7360 (m-40) cc_final: 0.6531 (t0) outliers start: 6 outliers final: 1 residues processed: 1058 average time/residue: 0.8860 time to fit residues: 1675.9920 Evaluate side-chains 758 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 756 time to evaluate : 9.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1469 random chunks: chunk 477 optimal weight: 7.9990 chunk 1278 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 833 optimal weight: 30.0000 chunk 350 optimal weight: 10.0000 chunk 1421 optimal weight: 9.9990 chunk 1179 optimal weight: 20.0000 chunk 658 optimal weight: 30.0000 chunk 118 optimal weight: 30.0000 chunk 470 optimal weight: 10.0000 chunk 746 optimal weight: 8.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A 580 ASN A 581 GLN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1759 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** B 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 934 GLN ** B1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS D 492 ASN ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 800 GLN ** D 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 864 GLN D 908 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS ** G 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 GLN ** H 892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 970 ASN ** H 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 GLN P 72 GLN ** P 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 293 ASN 1 441 GLN 1 654 HIS 1 746 ASN ** 1 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11101 GLN 11462 GLN 2 43 GLN 2 197 GLN ** 2 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 32 ASN 3 265 HIS ** 7 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 GLN ** 7 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 352 HIS i 27 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.155 115356 Z= 0.653 Angle : 0.898 17.961 156718 Z= 0.459 Chirality : 0.050 0.295 17924 Planarity : 0.006 0.077 20059 Dihedral : 9.986 169.989 16886 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.97 % Favored : 92.86 % Rotamer: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.14 % 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: -0.04 (0.07), residues: 14510 helix: 1.09 (0.06), residues: 7912 sheet: -0.83 (0.15), residues: 1172 loop : -1.52 (0.08), residues: 5426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP P 450 HIS 0.024 0.002 HIS 2 716 PHE 0.063 0.003 PHE G 165 TYR 0.045 0.003 TYR B1118 ARG 0.016 0.001 ARG 21050 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 879 time to evaluate : 9.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 MET cc_start: 0.8091 (mmt) cc_final: 0.7837 (mmp) REVERT: A 765 MET cc_start: 0.8926 (ptp) cc_final: 0.8368 (ptp) REVERT: A 791 MET cc_start: 0.7973 (ttt) cc_final: 0.7406 (mtt) REVERT: A 1864 MET cc_start: 0.8107 (mmp) cc_final: 0.7609 (mmm) REVERT: A 1883 MET cc_start: 0.8387 (tmm) cc_final: 0.7776 (tmm) REVERT: A 2051 MET cc_start: 0.8559 (pmm) cc_final: 0.7974 (tmm) REVERT: B 147 LEU cc_start: 0.9393 (mp) cc_final: 0.9076 (mt) REVERT: B 343 LEU cc_start: 0.8873 (pp) cc_final: 0.8562 (pp) REVERT: B 483 VAL cc_start: 0.9699 (t) cc_final: 0.9496 (p) REVERT: B 684 MET cc_start: 0.9006 (mmm) cc_final: 0.8347 (tpp) REVERT: D 449 LEU cc_start: 0.8821 (pt) cc_final: 0.8543 (pp) REVERT: E 639 LEU cc_start: 0.7814 (tp) cc_final: 0.7431 (pt) REVERT: F 52 LEU cc_start: 0.8563 (tp) cc_final: 0.8241 (tp) REVERT: F 559 MET cc_start: 0.7679 (mpp) cc_final: 0.7238 (mtm) REVERT: G 536 MET cc_start: 0.8027 (mmm) cc_final: 0.7725 (mmm) REVERT: G 696 ASP cc_start: 0.8085 (p0) cc_final: 0.7739 (p0) REVERT: H 471 ASP cc_start: 0.8776 (p0) cc_final: 0.8567 (p0) REVERT: H 615 MET cc_start: 0.8026 (mmp) cc_final: 0.7522 (mmp) REVERT: H 648 MET cc_start: 0.8737 (ppp) cc_final: 0.8116 (ppp) REVERT: I 107 MET cc_start: 0.9136 (ppp) cc_final: 0.8888 (ppp) REVERT: I 250 MET cc_start: 0.8095 (tmm) cc_final: 0.7774 (tmm) REVERT: K 35 MET cc_start: 0.8145 (ppp) cc_final: 0.7925 (ppp) REVERT: K 420 MET cc_start: 0.8250 (mmt) cc_final: 0.7796 (mtp) REVERT: P 261 TYR cc_start: 0.8464 (t80) cc_final: 0.8240 (t80) REVERT: Q 223 ASP cc_start: 0.8678 (p0) cc_final: 0.8162 (p0) REVERT: Q 249 ASN cc_start: 0.7855 (t0) cc_final: 0.7576 (t0) REVERT: 1 78 MET cc_start: 0.8003 (mpp) cc_final: 0.7471 (mpp) REVERT: 1 467 MET cc_start: 0.8107 (mtp) cc_final: 0.7759 (mtp) REVERT: 1 660 MET cc_start: 0.8621 (mpp) cc_final: 0.8271 (mpp) REVERT: 1 920 PHE cc_start: 0.6691 (m-80) cc_final: 0.6454 (m-80) REVERT: 1 1086 MET cc_start: 0.8704 (mmm) cc_final: 0.8319 (mmm) REVERT: 1 1309 MET cc_start: 0.8078 (pmm) cc_final: 0.7756 (pmm) REVERT: 2 390 ASN cc_start: 0.8202 (m-40) cc_final: 0.7835 (m110) REVERT: 2 594 MET cc_start: 0.8838 (pmm) cc_final: 0.8443 (pmm) REVERT: 2 764 MET cc_start: 0.7572 (tmm) cc_final: 0.7164 (tmm) REVERT: 2 1092 ASP cc_start: 0.7880 (m-30) cc_final: 0.7347 (m-30) REVERT: 4 90 TYR cc_start: 0.8613 (m-80) cc_final: 0.8213 (m-80) REVERT: 6 43 VAL cc_start: 0.8646 (p) cc_final: 0.8415 (p) REVERT: 7 49 ASP cc_start: 0.9206 (p0) cc_final: 0.8650 (p0) REVERT: 7 103 ARG cc_start: 0.7733 (ptt-90) cc_final: 0.7495 (ptt-90) REVERT: 9 38 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8010 (tm-30) REVERT: a 44 MET cc_start: 0.7879 (tpp) cc_final: 0.7613 (tpp) REVERT: e 125 ARG cc_start: 0.7645 (tpm170) cc_final: 0.7388 (mmt180) REVERT: g 245 MET cc_start: 0.7139 (ppp) cc_final: 0.6253 (ppp) REVERT: g 425 MET cc_start: 0.8266 (tmm) cc_final: 0.7697 (ptp) REVERT: g 585 ASN cc_start: 0.7527 (m-40) cc_final: 0.6601 (t0) outliers start: 5 outliers final: 3 residues processed: 883 average time/residue: 0.8922 time to fit residues: 1408.4122 Evaluate side-chains 692 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 689 time to evaluate : 8.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1469 random chunks: chunk 1370 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 809 optimal weight: 30.0000 chunk 1037 optimal weight: 0.7980 chunk 804 optimal weight: 30.0000 chunk 1196 optimal weight: 0.9990 chunk 793 optimal weight: 20.0000 chunk 1415 optimal weight: 1.9990 chunk 886 optimal weight: 0.0050 chunk 863 optimal weight: 0.8980 chunk 653 optimal weight: 4.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 ASN D 908 GLN ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 HIS ** G 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 HIS ** G 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 HIS ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 ASN ** P 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 HIS ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 313 HIS ** 1 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 531 ASN 1 746 ASN ** 11462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 116 GLN 6 29 HIS 6 126 GLN ** 7 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 118 GLN ** e 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 115356 Z= 0.183 Angle : 0.611 13.420 156718 Z= 0.311 Chirality : 0.042 0.198 17924 Planarity : 0.004 0.086 20059 Dihedral : 9.684 169.234 16886 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 0.02 % Allowed : 1.49 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.14 % 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: 0.53 (0.07), residues: 14510 helix: 1.55 (0.06), residues: 7878 sheet: -0.65 (0.15), residues: 1196 loop : -1.19 (0.09), residues: 5436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP j 180 HIS 0.015 0.001 HIS H 894 PHE 0.050 0.002 PHE g 333 TYR 0.031 0.001 TYR I 182 ARG 0.015 0.000 ARG B 808 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1019 time to evaluate : 9.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8182 (ppp) cc_final: 0.7853 (ppp) REVERT: A 549 MET cc_start: 0.8011 (mmt) cc_final: 0.7795 (mmp) REVERT: A 765 MET cc_start: 0.8838 (ptp) cc_final: 0.8396 (ptp) REVERT: A 791 MET cc_start: 0.7951 (ttt) cc_final: 0.7473 (mtt) REVERT: A 1864 MET cc_start: 0.8041 (mmp) cc_final: 0.7550 (mmm) REVERT: A 1883 MET cc_start: 0.8070 (tmm) cc_final: 0.7513 (tmm) REVERT: A 2051 MET cc_start: 0.8413 (pmm) cc_final: 0.7947 (tmm) REVERT: B 211 LEU cc_start: 0.9394 (pp) cc_final: 0.9061 (tp) REVERT: B 343 LEU cc_start: 0.8804 (pp) cc_final: 0.8596 (pp) REVERT: B 684 MET cc_start: 0.8786 (mmm) cc_final: 0.7928 (tpp) REVERT: B 1020 TYR cc_start: 0.8672 (p90) cc_final: 0.8367 (p90) REVERT: B 1065 CYS cc_start: 0.8141 (m) cc_final: 0.7862 (m) REVERT: D 787 LEU cc_start: 0.8901 (mt) cc_final: 0.8698 (mt) REVERT: D 826 GLU cc_start: 0.7996 (pm20) cc_final: 0.7655 (pm20) REVERT: D 848 ASP cc_start: 0.7477 (m-30) cc_final: 0.7255 (m-30) REVERT: D 874 MET cc_start: 0.8775 (tpp) cc_final: 0.8481 (tpp) REVERT: E 639 LEU cc_start: 0.7902 (tp) cc_final: 0.7573 (pt) REVERT: F 559 MET cc_start: 0.7703 (mpp) cc_final: 0.7248 (mtm) REVERT: G 696 ASP cc_start: 0.7627 (p0) cc_final: 0.7336 (p0) REVERT: G 931 LEU cc_start: 0.8996 (mp) cc_final: 0.8750 (mp) REVERT: H 329 VAL cc_start: 0.9187 (t) cc_final: 0.8908 (p) REVERT: H 471 ASP cc_start: 0.8638 (p0) cc_final: 0.8419 (p0) REVERT: H 535 MET cc_start: 0.8339 (ppp) cc_final: 0.8073 (ppp) REVERT: H 615 MET cc_start: 0.7773 (mmp) cc_final: 0.7340 (mmp) REVERT: H 648 MET cc_start: 0.8774 (ppp) cc_final: 0.8263 (ppp) REVERT: I 250 MET cc_start: 0.8066 (tmm) cc_final: 0.7719 (tmm) REVERT: K 299 MET cc_start: 0.8248 (mmm) cc_final: 0.8011 (tmm) REVERT: K 420 MET cc_start: 0.8079 (mmt) cc_final: 0.7645 (mtp) REVERT: Q 223 ASP cc_start: 0.8272 (p0) cc_final: 0.7593 (p0) REVERT: 1 78 MET cc_start: 0.7671 (mpp) cc_final: 0.7147 (mpp) REVERT: 1 238 MET cc_start: 0.7491 (ppp) cc_final: 0.6392 (pmm) REVERT: 1 470 MET cc_start: 0.8210 (mmt) cc_final: 0.7889 (mmt) REVERT: 1 637 MET cc_start: 0.7806 (ppp) cc_final: 0.6918 (ppp) REVERT: 1 920 PHE cc_start: 0.6361 (m-80) cc_final: 0.6130 (m-80) REVERT: 2 155 MET cc_start: 0.7620 (ptp) cc_final: 0.7163 (ptp) REVERT: 2 529 MET cc_start: 0.7965 (mmm) cc_final: 0.7628 (mmm) REVERT: 2 1092 ASP cc_start: 0.7610 (m-30) cc_final: 0.6992 (m-30) REVERT: 4 90 TYR cc_start: 0.8499 (m-80) cc_final: 0.8060 (m-80) REVERT: 5 61 GLU cc_start: 0.8585 (mp0) cc_final: 0.8369 (mp0) REVERT: 6 92 MET cc_start: 0.6408 (mtt) cc_final: 0.6068 (mtt) REVERT: 7 49 ASP cc_start: 0.9090 (p0) cc_final: 0.8526 (p0) REVERT: 7 103 ARG cc_start: 0.7773 (ptt-90) cc_final: 0.7492 (ptt-90) REVERT: 9 42 LEU cc_start: 0.8626 (mm) cc_final: 0.8381 (mm) REVERT: g 425 MET cc_start: 0.8085 (tmm) cc_final: 0.7604 (ptp) REVERT: g 585 ASN cc_start: 0.7435 (m-40) cc_final: 0.6506 (t0) REVERT: j 451 MET cc_start: 0.8648 (mmp) cc_final: 0.8326 (mmp) outliers start: 2 outliers final: 0 residues processed: 1021 average time/residue: 0.9065 time to fit residues: 1649.2674 Evaluate side-chains 731 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 731 time to evaluate : 9.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1469 random chunks: chunk 875 optimal weight: 0.9980 chunk 565 optimal weight: 3.9990 chunk 845 optimal weight: 3.9990 chunk 426 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 274 optimal weight: 0.6980 chunk 900 optimal weight: 5.9990 chunk 964 optimal weight: 7.9990 chunk 700 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 1112 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 232 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN D 289 HIS D 492 ASN D 625 GLN D 800 GLN ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 HIS ** G 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 ASN ** P 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 96 HIS 1 531 ASN 1 746 ASN 1 825 ASN 11093 GLN 11310 HIS 2 390 ASN ** 2 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 21097 HIS ** 3 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 265 HIS 7 74 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 519 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 115356 Z= 0.174 Angle : 0.592 13.386 156718 Z= 0.300 Chirality : 0.041 0.220 17924 Planarity : 0.004 0.059 20059 Dihedral : 9.547 169.874 16886 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.05 % Favored : 94.82 % Rotamer: Outliers : 0.03 % Allowed : 1.19 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.69 (0.07), residues: 14510 helix: 1.65 (0.06), residues: 7880 sheet: -0.50 (0.15), residues: 1193 loop : -1.11 (0.09), residues: 5437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 455 HIS 0.011 0.001 HIS H 894 PHE 0.043 0.001 PHE g 333 TYR 0.026 0.001 TYR g 545 ARG 0.010 0.000 ARG 1 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 994 time to evaluate : 9.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8168 (ppp) cc_final: 0.7854 (ppp) REVERT: A 765 MET cc_start: 0.8856 (ptp) cc_final: 0.8416 (ptp) REVERT: A 791 MET cc_start: 0.7948 (ttt) cc_final: 0.7512 (mtt) REVERT: A 1286 MET cc_start: 0.8844 (mpp) cc_final: 0.8641 (mpp) REVERT: A 1864 MET cc_start: 0.8033 (mmp) cc_final: 0.7603 (mmm) REVERT: A 1883 MET cc_start: 0.8058 (tmm) cc_final: 0.7470 (tmm) REVERT: B 211 LEU cc_start: 0.9359 (pp) cc_final: 0.9074 (tp) REVERT: B 435 MET cc_start: 0.7928 (tpp) cc_final: 0.7477 (tpp) REVERT: B 684 MET cc_start: 0.8773 (mmm) cc_final: 0.8288 (tpp) REVERT: B 854 MET cc_start: 0.7853 (mtp) cc_final: 0.7619 (mtp) REVERT: B 1020 TYR cc_start: 0.8571 (p90) cc_final: 0.8253 (p90) REVERT: B 1065 CYS cc_start: 0.8086 (m) cc_final: 0.7794 (m) REVERT: D 173 LEU cc_start: 0.9072 (tp) cc_final: 0.8861 (tp) REVERT: D 848 ASP cc_start: 0.7603 (m-30) cc_final: 0.7358 (m-30) REVERT: D 874 MET cc_start: 0.8739 (tpp) cc_final: 0.8446 (tpp) REVERT: E 810 LYS cc_start: 0.8490 (tptm) cc_final: 0.8071 (tptp) REVERT: F 379 LEU cc_start: 0.9103 (tp) cc_final: 0.8815 (pt) REVERT: F 434 MET cc_start: 0.8596 (mmp) cc_final: 0.8374 (mmm) REVERT: F 559 MET cc_start: 0.7816 (mpp) cc_final: 0.7311 (mtm) REVERT: G 125 MET cc_start: 0.8353 (tpp) cc_final: 0.7311 (tpp) REVERT: G 696 ASP cc_start: 0.7549 (p0) cc_final: 0.7277 (p0) REVERT: G 893 LEU cc_start: 0.9298 (tp) cc_final: 0.9014 (tp) REVERT: H 329 VAL cc_start: 0.9152 (t) cc_final: 0.8881 (p) REVERT: H 471 ASP cc_start: 0.8681 (p0) cc_final: 0.8464 (p0) REVERT: H 535 MET cc_start: 0.8316 (ppp) cc_final: 0.8074 (ppp) REVERT: H 648 MET cc_start: 0.8720 (ppp) cc_final: 0.8218 (ppp) REVERT: I 250 MET cc_start: 0.8097 (tmm) cc_final: 0.7751 (tmm) REVERT: K 35 MET cc_start: 0.7644 (ppp) cc_final: 0.7400 (ppp) REVERT: K 420 MET cc_start: 0.7916 (mmt) cc_final: 0.7523 (mtp) REVERT: Q 223 ASP cc_start: 0.8273 (p0) cc_final: 0.7589 (p0) REVERT: Q 249 ASN cc_start: 0.7750 (t0) cc_final: 0.7261 (t0) REVERT: 1 78 MET cc_start: 0.7606 (mpp) cc_final: 0.7065 (mpp) REVERT: 1 238 MET cc_start: 0.7361 (ppp) cc_final: 0.6442 (pmm) REVERT: 1 470 MET cc_start: 0.7944 (mmt) cc_final: 0.7641 (mmt) REVERT: 1 660 MET cc_start: 0.8616 (mpp) cc_final: 0.7844 (mpp) REVERT: 1 1309 MET cc_start: 0.8199 (pmm) cc_final: 0.7932 (pmm) REVERT: 2 155 MET cc_start: 0.7608 (ptp) cc_final: 0.7105 (ptp) REVERT: 2 297 MET cc_start: 0.8362 (ptt) cc_final: 0.8108 (pmm) REVERT: 2 1092 ASP cc_start: 0.7611 (m-30) cc_final: 0.7148 (m-30) REVERT: 4 90 TYR cc_start: 0.8538 (m-80) cc_final: 0.8152 (m-80) REVERT: 5 61 GLU cc_start: 0.8489 (mp0) cc_final: 0.8163 (mp0) REVERT: 6 92 MET cc_start: 0.6275 (mtt) cc_final: 0.5993 (mtt) REVERT: 7 49 ASP cc_start: 0.9081 (p0) cc_final: 0.8478 (p0) REVERT: 9 42 LEU cc_start: 0.8592 (mm) cc_final: 0.8390 (mm) REVERT: g 425 MET cc_start: 0.8087 (tmm) cc_final: 0.7713 (ptp) REVERT: g 585 ASN cc_start: 0.7233 (m-40) cc_final: 0.6384 (t0) REVERT: j 451 MET cc_start: 0.8634 (mmp) cc_final: 0.8302 (mmp) REVERT: k 156 ASP cc_start: 0.7534 (t70) cc_final: 0.7285 (t0) REVERT: l 84 ARG cc_start: 0.8149 (mmp80) cc_final: 0.7683 (mmp80) outliers start: 4 outliers final: 1 residues processed: 996 average time/residue: 0.8619 time to fit residues: 1540.5073 Evaluate side-chains 749 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 748 time to evaluate : 9.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1469 random chunks: chunk 1287 optimal weight: 50.0000 chunk 1356 optimal weight: 5.9990 chunk 1237 optimal weight: 0.0030 chunk 1319 optimal weight: 8.9990 chunk 794 optimal weight: 20.0000 chunk 574 optimal weight: 0.7980 chunk 1036 optimal weight: 6.9990 chunk 404 optimal weight: 30.0000 chunk 1192 optimal weight: 1.9990 chunk 1247 optimal weight: 10.0000 chunk 1314 optimal weight: 9.9990 overall best weight: 3.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2152 GLN B 232 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1002 HIS D 492 ASN D 818 HIS ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 ASN ** P 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 441 GLN ** 1 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 746 ASN ** 1 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 126 GLN 7 74 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 115356 Z= 0.270 Angle : 0.627 13.883 156718 Z= 0.318 Chirality : 0.042 0.363 17924 Planarity : 0.004 0.064 20059 Dihedral : 9.560 171.491 16886 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.58 % Favored : 94.30 % Rotamer: Outliers : 0.01 % Allowed : 0.71 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.14 % 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: 0.67 (0.07), residues: 14510 helix: 1.64 (0.06), residues: 7878 sheet: -0.50 (0.15), residues: 1185 loop : -1.14 (0.09), residues: 5447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 455 HIS 0.020 0.001 HIS D 568 PHE 0.040 0.002 PHE g 333 TYR 0.028 0.001 TYR 11797 ARG 0.009 0.000 ARG 1 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 944 time to evaluate : 9.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.8535 (mmt) cc_final: 0.8202 (mmt) REVERT: A 531 MET cc_start: 0.5942 (tpt) cc_final: 0.5715 (tpp) REVERT: A 765 MET cc_start: 0.8844 (ptp) cc_final: 0.8410 (ptp) REVERT: A 791 MET cc_start: 0.7986 (ttt) cc_final: 0.7556 (mtt) REVERT: A 1286 MET cc_start: 0.8892 (mpp) cc_final: 0.8669 (mpp) REVERT: A 1864 MET cc_start: 0.8063 (mmp) cc_final: 0.7655 (mmm) REVERT: A 1883 MET cc_start: 0.8195 (tmm) cc_final: 0.7587 (tmm) REVERT: A 2051 MET cc_start: 0.8484 (pmm) cc_final: 0.7876 (tmm) REVERT: B 211 LEU cc_start: 0.9395 (pp) cc_final: 0.9082 (tp) REVERT: B 452 MET cc_start: 0.8375 (ppp) cc_final: 0.8165 (ppp) REVERT: B 684 MET cc_start: 0.8930 (mmm) cc_final: 0.8455 (tpp) REVERT: B 1101 MET cc_start: 0.7879 (mtp) cc_final: 0.7523 (mtp) REVERT: B 1190 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7556 (tm-30) REVERT: D 449 LEU cc_start: 0.8699 (pt) cc_final: 0.8344 (pp) REVERT: D 848 ASP cc_start: 0.7951 (m-30) cc_final: 0.7716 (m-30) REVERT: D 874 MET cc_start: 0.8762 (tpp) cc_final: 0.8422 (tpp) REVERT: F 52 LEU cc_start: 0.8483 (tp) cc_final: 0.8265 (tp) REVERT: F 379 LEU cc_start: 0.9141 (tp) cc_final: 0.8845 (pt) REVERT: F 559 MET cc_start: 0.7720 (mpp) cc_final: 0.7191 (mtm) REVERT: G 125 MET cc_start: 0.8489 (tpp) cc_final: 0.7347 (tpp) REVERT: G 696 ASP cc_start: 0.7628 (p0) cc_final: 0.7293 (p0) REVERT: G 893 LEU cc_start: 0.9360 (tp) cc_final: 0.9091 (tp) REVERT: H 329 VAL cc_start: 0.9186 (t) cc_final: 0.8919 (p) REVERT: H 471 ASP cc_start: 0.8687 (p0) cc_final: 0.8475 (p0) REVERT: H 535 MET cc_start: 0.8327 (ppp) cc_final: 0.8101 (ppp) REVERT: H 648 MET cc_start: 0.8705 (ppp) cc_final: 0.8217 (ppp) REVERT: I 107 MET cc_start: 0.9085 (ppp) cc_final: 0.8749 (tmm) REVERT: I 250 MET cc_start: 0.8127 (tmm) cc_final: 0.7768 (tmm) REVERT: K 35 MET cc_start: 0.7829 (ppp) cc_final: 0.7552 (ppp) REVERT: K 420 MET cc_start: 0.8054 (mmt) cc_final: 0.7592 (mtp) REVERT: Q 17 LEU cc_start: 0.9557 (mt) cc_final: 0.9354 (mt) REVERT: Q 223 ASP cc_start: 0.8358 (p0) cc_final: 0.7742 (p0) REVERT: Q 249 ASN cc_start: 0.7825 (t0) cc_final: 0.7395 (t0) REVERT: 1 78 MET cc_start: 0.7715 (mpp) cc_final: 0.7174 (mpp) REVERT: 1 238 MET cc_start: 0.7324 (ppp) cc_final: 0.7121 (ppp) REVERT: 1 660 MET cc_start: 0.8583 (mpp) cc_final: 0.7836 (mpp) REVERT: 1 725 LEU cc_start: 0.8476 (tt) cc_final: 0.8084 (mp) REVERT: 1 1073 GLU cc_start: 0.8232 (tm-30) cc_final: 0.8005 (tm-30) REVERT: 1 1309 MET cc_start: 0.8210 (pmm) cc_final: 0.7873 (pmm) REVERT: 2 155 MET cc_start: 0.7634 (ptp) cc_final: 0.7224 (ptp) REVERT: 2 297 MET cc_start: 0.8508 (ptt) cc_final: 0.8110 (pmm) REVERT: 2 529 MET cc_start: 0.8157 (mmm) cc_final: 0.7937 (mmm) REVERT: 2 1092 ASP cc_start: 0.7679 (m-30) cc_final: 0.7137 (m-30) REVERT: 4 90 TYR cc_start: 0.8588 (m-80) cc_final: 0.8239 (m-80) REVERT: 5 61 GLU cc_start: 0.8586 (mp0) cc_final: 0.8281 (mp0) REVERT: 7 49 ASP cc_start: 0.9126 (p0) cc_final: 0.8532 (p0) REVERT: 8 55 LEU cc_start: 0.9061 (mp) cc_final: 0.8727 (mp) REVERT: g 245 MET cc_start: 0.7360 (ppp) cc_final: 0.6462 (ppp) REVERT: g 425 MET cc_start: 0.8137 (tmm) cc_final: 0.7821 (ptp) REVERT: g 585 ASN cc_start: 0.7531 (m-40) cc_final: 0.6580 (t0) REVERT: k 156 ASP cc_start: 0.7611 (t70) cc_final: 0.7366 (t0) outliers start: 1 outliers final: 0 residues processed: 945 average time/residue: 0.8995 time to fit residues: 1526.4951 Evaluate side-chains 731 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 731 time to evaluate : 9.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1469 random chunks: chunk 866 optimal weight: 0.5980 chunk 1395 optimal weight: 0.0470 chunk 851 optimal weight: 7.9990 chunk 661 optimal weight: 6.9990 chunk 969 optimal weight: 2.9990 chunk 1463 optimal weight: 50.0000 chunk 1346 optimal weight: 50.0000 chunk 1165 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 900 optimal weight: 0.9990 chunk 714 optimal weight: 0.9980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS D 492 ASN ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN ** G 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 HIS ** G 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 445 ASN H 609 GLN H 613 ASN ** H 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 970 ASN ** H 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 ASN ** P 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 441 GLN ** 1 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 746 ASN ** 2 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 265 HIS 6 126 GLN ** 7 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 GLN 7 100 HIS ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 519 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 115356 Z= 0.166 Angle : 0.596 13.172 156718 Z= 0.299 Chirality : 0.041 0.339 17924 Planarity : 0.004 0.059 20059 Dihedral : 9.472 171.222 16886 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.77 (0.07), residues: 14510 helix: 1.72 (0.06), residues: 7876 sheet: -0.44 (0.15), residues: 1187 loop : -1.08 (0.09), residues: 5447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 455 HIS 0.014 0.001 HIS 7 100 PHE 0.037 0.001 PHE g 333 TYR 0.029 0.001 TYR H 326 ARG 0.024 0.000 ARG i 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29020 Ramachandran restraints generated. 14510 Oldfield, 0 Emsley, 14510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 996 time to evaluate : 9.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 MET cc_start: 0.5819 (tpt) cc_final: 0.5607 (tpp) REVERT: A 765 MET cc_start: 0.8823 (ptp) cc_final: 0.8406 (ptp) REVERT: A 791 MET cc_start: 0.8063 (ttt) cc_final: 0.7719 (mtt) REVERT: A 1286 MET cc_start: 0.8848 (mpp) cc_final: 0.8639 (mpp) REVERT: A 1864 MET cc_start: 0.7965 (mmp) cc_final: 0.7545 (mmm) REVERT: A 1883 MET cc_start: 0.8061 (tmm) cc_final: 0.7453 (tmm) REVERT: A 2051 MET cc_start: 0.8453 (pmm) cc_final: 0.7820 (tmm) REVERT: B 211 LEU cc_start: 0.9393 (pp) cc_final: 0.9064 (tp) REVERT: B 343 LEU cc_start: 0.8906 (pp) cc_final: 0.8386 (pp) REVERT: B 435 MET cc_start: 0.8002 (tpp) cc_final: 0.7339 (tpp) REVERT: B 684 MET cc_start: 0.8802 (mmm) cc_final: 0.8294 (tpp) REVERT: B 1020 TYR cc_start: 0.8490 (p90) cc_final: 0.8149 (p90) REVERT: B 1065 CYS cc_start: 0.8121 (m) cc_final: 0.7698 (m) REVERT: D 173 LEU cc_start: 0.9089 (tp) cc_final: 0.8871 (tp) REVERT: D 289 HIS cc_start: 0.6695 (OUTLIER) cc_final: 0.6485 (m90) REVERT: D 449 LEU cc_start: 0.8671 (pt) cc_final: 0.8307 (pp) REVERT: D 848 ASP cc_start: 0.7898 (m-30) cc_final: 0.7266 (m-30) REVERT: D 874 MET cc_start: 0.8674 (tpp) cc_final: 0.8394 (tpp) REVERT: F 379 LEU cc_start: 0.9114 (tp) cc_final: 0.8816 (pt) REVERT: F 559 MET cc_start: 0.7675 (mpp) cc_final: 0.7181 (mtm) REVERT: G 38 LEU cc_start: 0.8724 (pp) cc_final: 0.8384 (tt) REVERT: G 125 MET cc_start: 0.8471 (tpp) cc_final: 0.7360 (tpp) REVERT: G 458 MET cc_start: 0.8781 (mmm) cc_final: 0.8562 (mmt) REVERT: G 536 MET cc_start: 0.7686 (mmm) cc_final: 0.7419 (mmm) REVERT: G 696 ASP cc_start: 0.7530 (p0) cc_final: 0.7271 (p0) REVERT: G 893 LEU cc_start: 0.9272 (tp) cc_final: 0.8949 (tp) REVERT: H 471 ASP cc_start: 0.8657 (p0) cc_final: 0.8441 (p0) REVERT: H 535 MET cc_start: 0.8247 (ppp) cc_final: 0.8038 (ppp) REVERT: H 648 MET cc_start: 0.8665 (ppp) cc_final: 0.8174 (ppp) REVERT: I 250 MET cc_start: 0.8073 (tmm) cc_final: 0.7665 (tmm) REVERT: K 35 MET cc_start: 0.7760 (ppp) cc_final: 0.7430 (ppp) REVERT: K 92 MET cc_start: 0.8660 (ppp) cc_final: 0.8440 (ppp) REVERT: K 420 MET cc_start: 0.8026 (mmt) cc_final: 0.7577 (mtp) REVERT: P 427 MET cc_start: 0.8558 (tmm) cc_final: 0.8335 (tmm) REVERT: Q 223 ASP cc_start: 0.8193 (p0) cc_final: 0.7556 (p0) REVERT: Q 249 ASN cc_start: 0.7725 (t0) cc_final: 0.7190 (t0) REVERT: 1 78 MET cc_start: 0.7679 (mpp) cc_final: 0.7151 (mpp) REVERT: 1 238 MET cc_start: 0.7343 (ppp) cc_final: 0.6547 (pmm) REVERT: 1 637 MET cc_start: 0.7800 (ppp) cc_final: 0.7334 (ppp) REVERT: 1 725 LEU cc_start: 0.8452 (tt) cc_final: 0.8135 (mp) REVERT: 1 899 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7040 (mt-10) REVERT: 1 1309 MET cc_start: 0.8193 (pmm) cc_final: 0.7919 (pmm) REVERT: 2 155 MET cc_start: 0.7569 (ptp) cc_final: 0.7111 (ptp) REVERT: 2 297 MET cc_start: 0.8505 (ptt) cc_final: 0.8181 (pmm) REVERT: 2 298 MET cc_start: 0.8657 (ttp) cc_final: 0.8412 (ttp) REVERT: 2 594 MET cc_start: 0.8488 (pmm) cc_final: 0.8097 (pmm) REVERT: 2 747 LEU cc_start: 0.9211 (mm) cc_final: 0.8483 (tt) REVERT: 2 1092 ASP cc_start: 0.7467 (m-30) cc_final: 0.7131 (m-30) REVERT: 4 18 MET cc_start: 0.7764 (mpp) cc_final: 0.7551 (mpp) REVERT: 4 90 TYR cc_start: 0.8531 (m-80) cc_final: 0.8161 (m-80) REVERT: 5 61 GLU cc_start: 0.8419 (mp0) cc_final: 0.8079 (mp0) REVERT: 7 49 ASP cc_start: 0.9104 (p0) cc_final: 0.8504 (p0) REVERT: 8 55 LEU cc_start: 0.8971 (mp) cc_final: 0.8580 (mp) REVERT: 9 42 LEU cc_start: 0.8558 (mm) cc_final: 0.8303 (mm) REVERT: g 245 MET cc_start: 0.7243 (ppp) cc_final: 0.6341 (ppp) REVERT: g 425 MET cc_start: 0.8090 (tmm) cc_final: 0.7792 (ptp) REVERT: g 585 ASN cc_start: 0.7463 (m-40) cc_final: 0.6516 (t0) REVERT: j 451 MET cc_start: 0.8616 (mmp) cc_final: 0.8283 (mmp) REVERT: k 156 ASP cc_start: 0.7467 (t70) cc_final: 0.7203 (t0) outliers start: 5 outliers final: 1 residues processed: 999 average time/residue: 0.8958 time to fit residues: 1612.9182 Evaluate side-chains 757 residues out of total 12944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 755 time to evaluate : 9.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1469 random chunks: chunk 925 optimal weight: 6.9990 chunk 1241 optimal weight: 0.9990 chunk 357 optimal weight: 1.9990 chunk 1074 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 323 optimal weight: 0.0370 chunk 1167 optimal weight: 9.9990 chunk 488 optimal weight: 9.9990 chunk 1198 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 HIS D 492 ASN ** D 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 670 GLN ** G 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 ASN ** P 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 441 GLN ** 1 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 746 ASN ** 11462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 21097 HIS 3 262 GLN 6 126 GLN ** 7 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 4 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.097015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.068337 restraints weight = 472575.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066566 restraints weight = 322281.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.066634 restraints weight = 287026.052| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 115356 Z= 0.239 Angle : 0.613 14.349 156718 Z= 0.309 Chirality : 0.042 0.308 17924 Planarity : 0.004 0.057 20059 Dihedral : 9.478 172.516 16886 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.40 % Favored : 94.48 % Rotamer: Outliers : 0.02 % Allowed : 0.32 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.76 (0.07), residues: 14510 helix: 1.71 (0.06), residues: 7888 sheet: -0.45 (0.15), residues: 1196 loop : -1.10 (0.09), residues: 5426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B 455 HIS 0.013 0.001 HIS D 223 PHE 0.035 0.002 PHE A2104 TYR 0.031 0.001 TYR H 326 ARG 0.017 0.000 ARG i 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24562.55 seconds wall clock time: 431 minutes 34.86 seconds (25894.86 seconds total)