Starting phenix.real_space_refine on Mon Dec 30 11:38:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7emf_31191/12_2024/7emf_31191.cif Found real_map, /net/cci-nas-00/data/ceres_data/7emf_31191/12_2024/7emf_31191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7emf_31191/12_2024/7emf_31191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7emf_31191/12_2024/7emf_31191.map" model { file = "/net/cci-nas-00/data/ceres_data/7emf_31191/12_2024/7emf_31191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7emf_31191/12_2024/7emf_31191.cif" } resolution = 3.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 396 5.16 5 C 39692 2.51 5 N 10786 2.21 5 O 11458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 62334 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 3578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3578 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 30, 'TRANS': 436} Chain breaks: 5 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "D" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1268 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Chain: "F" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1374 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 9, 'TRANS': 157} Chain breaks: 1 Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1348 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 10, 'TRANS': 150} Chain: "H" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain breaks: 1 Chain: "I" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 605 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Chain: "J" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 840 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 100 Chain: "K" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 879 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "N" Number of atoms: 7772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7772 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 61, 'TRANS': 955} Chain breaks: 10 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "O" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1226 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 16, 'TRANS': 140} Chain breaks: 1 Chain: "P" Number of atoms: 5983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5983 Classifications: {'peptide': 766} Link IDs: {'PTRANS': 38, 'TRANS': 727} Chain breaks: 4 Chain: "Q" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4361 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 27, 'TRANS': 523} Chain breaks: 5 Chain: "R" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1532 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 8, 'TRANS': 182} Chain: "S" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 476 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 7, 'TRANS': 67} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "T" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1499 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "U" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "V" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1063 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain: "W" Number of atoms: 10774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10774 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 70, 'TRANS': 1263} Chain: "X" Number of atoms: 7061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 7061 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 35, 'TRANS': 861} Chain breaks: 9 Chain: "Y" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1605 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 15, 'TRANS': 194} Chain breaks: 1 Chain: "Z" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 765 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain breaks: 1 Chain: "0" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2159 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 9, 'TRANS': 257} Chain breaks: 2 Chain: "1" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 1 Chain: "2" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 899 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain breaks: 1 Chain: "3" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1022 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 3 Chain: "4" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 986 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" 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 26042 SG CYS P 798 138.828 251.501 60.753 1.00 61.26 S ATOM 26066 SG CYS P 801 141.463 249.004 61.101 1.00 68.86 S ATOM 26279 SG CYS P 827 142.780 252.646 61.643 1.00 67.73 S ATOM 26293 SG CYS P 829 141.139 251.768 58.034 1.00 67.16 S ATOM 58363 SG CYS 0 281 116.315 210.661 125.061 1.00 78.68 S ATOM 58389 SG CYS 0 284 115.359 213.470 127.432 1.00 81.40 S ATOM 58597 SG CYS 0 309 112.171 211.559 125.450 1.00 79.33 S Time building chain proxies: 25.43, per 1000 atoms: 0.41 Number of scatterers: 62334 At special positions: 0 Unit cell: (199.206, 381.548, 236.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 396 16.00 O 11458 8.00 N 10786 7.00 C 39692 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 - 3.00 Amino acid : True - 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: 11.57 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 401 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 281 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 284 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 309 " pdb=" ZN P 901 " pdb="ZN ZN P 901 " - pdb=" SG CYS P 829 " pdb="ZN ZN P 901 " - pdb=" SG CYS P 827 " pdb="ZN ZN P 901 " - pdb=" SG CYS P 798 " pdb="ZN ZN P 901 " - pdb=" SG CYS P 801 " Number of angles added : 6 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15156 Finding SS restraints... Secondary structure from input PDB file: 302 helices and 40 sheets defined 58.1% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'A' and resid 13 through 27 removed outlier: 3.824A pdb=" N SER A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 73 through 89 Processing helix chain 'A' and resid 135 through 144 removed outlier: 3.680A pdb=" N GLU A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 removed outlier: 3.612A pdb=" N PHE A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 195 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.940A pdb=" N LEU A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 403 through 423 Processing helix chain 'A' and resid 490 through 502 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.650A pdb=" N THR A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 518 " --> pdb=" O LYS A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 18 Processing helix chain 'D' and resid 27 through 52 Processing helix chain 'D' and resid 63 through 141 removed outlier: 4.019A pdb=" N GLN D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 157 Processing helix chain 'D' and resid 178 through 184 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'F' and resid 9 through 13 removed outlier: 3.652A pdb=" N ILE F 13 " --> pdb=" O LEU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 25 through 33 removed outlier: 4.097A pdb=" N LEU F 30 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 53 removed outlier: 4.005A pdb=" N VAL F 49 " --> pdb=" O CYS F 45 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN F 53 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 136 removed outlier: 3.826A pdb=" N VAL F 114 " --> pdb=" O ASP F 110 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER F 135 " --> pdb=" O ASP F 131 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 188 Processing helix chain 'G' and resid 18 through 26 removed outlier: 3.958A pdb=" N THR G 22 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 99 Processing helix chain 'G' and resid 103 through 125 removed outlier: 3.645A pdb=" N GLU G 107 " --> pdb=" O ILE G 103 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE G 123 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 175 removed outlier: 4.557A pdb=" N HIS G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Proline residue: G 172 - end of helix Processing helix chain 'H' and resid 4 through 36 Processing helix chain 'H' and resid 41 through 66 removed outlier: 3.578A pdb=" N GLU H 66 " --> pdb=" O VAL H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 94 removed outlier: 3.634A pdb=" N GLU H 94 " --> pdb=" O MET H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 109 Processing helix chain 'H' and resid 114 through 129 Processing helix chain 'H' and resid 134 through 158 Processing helix chain 'H' and resid 174 through 187 removed outlier: 3.559A pdb=" N PHE H 187 " --> pdb=" O ALA H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 79 Processing helix chain 'I' and resid 86 through 102 Processing helix chain 'I' and resid 110 through 138 Processing helix chain 'J' and resid 8 through 29 Processing helix chain 'J' and resid 35 through 60 removed outlier: 3.990A pdb=" N GLN J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 73 removed outlier: 4.042A pdb=" N PHE J 68 " --> pdb=" O PRO J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 117 Processing helix chain 'J' and resid 117 through 128 removed outlier: 3.553A pdb=" N MET J 121 " --> pdb=" O PHE J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 35 Processing helix chain 'K' and resid 41 through 73 Processing helix chain 'K' and resid 83 through 116 removed outlier: 3.768A pdb=" N ARG K 87 " --> pdb=" O SER K 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 73 Processing helix chain 'N' and resid 77 through 106 removed outlier: 3.897A pdb=" N ILE N 83 " --> pdb=" O VAL N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 142 removed outlier: 3.600A pdb=" N VAL N 112 " --> pdb=" O ASN N 108 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP N 142 " --> pdb=" O SER N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 162 removed outlier: 3.789A pdb=" N ALA N 157 " --> pdb=" O ALA N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 178 Processing helix chain 'N' and resid 186 through 204 Processing helix chain 'N' and resid 217 through 221 Processing helix chain 'N' and resid 267 through 284 Processing helix chain 'N' and resid 287 through 318 removed outlier: 3.860A pdb=" N ASP N 291 " --> pdb=" O LYS N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 382 through 389 removed outlier: 3.708A pdb=" N GLU N 387 " --> pdb=" O SER N 383 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 424 removed outlier: 3.529A pdb=" N LEU N 400 " --> pdb=" O SER N 396 " (cutoff:3.500A) Processing helix chain 'N' and resid 471 through 485 Processing helix chain 'N' and resid 488 through 507 removed outlier: 3.899A pdb=" N TRP N 492 " --> pdb=" O ARG N 488 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN N 494 " --> pdb=" O ILE N 490 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE N 498 " --> pdb=" O GLN N 494 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP N 499 " --> pdb=" O GLN N 495 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 652 removed outlier: 3.595A pdb=" N ALA N 642 " --> pdb=" O ASN N 638 " (cutoff:3.500A) Processing helix chain 'N' and resid 652 through 664 removed outlier: 4.038A pdb=" N GLY N 656 " --> pdb=" O MET N 652 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU N 657 " --> pdb=" O PRO N 653 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU N 664 " --> pdb=" O GLU N 660 " (cutoff:3.500A) Processing helix chain 'N' and resid 694 through 702 Processing helix chain 'N' and resid 714 through 718 removed outlier: 4.184A pdb=" N ARG N 718 " --> pdb=" O ARG N 715 " (cutoff:3.500A) Processing helix chain 'N' and resid 759 through 787 removed outlier: 3.841A pdb=" N VAL N 763 " --> pdb=" O GLY N 759 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS N 779 " --> pdb=" O ARG N 775 " (cutoff:3.500A) Processing helix chain 'N' and resid 793 through 797 Processing helix chain 'N' and resid 851 through 862 Processing helix chain 'N' and resid 864 through 883 removed outlier: 5.043A pdb=" N ALA N 877 " --> pdb=" O PHE N 873 " (cutoff:3.500A) Proline residue: N 878 - end of helix removed outlier: 3.647A pdb=" N ALA N 881 " --> pdb=" O ALA N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 958 through 967 removed outlier: 3.541A pdb=" N PHE N 962 " --> pdb=" O GLY N 958 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE N 966 " --> pdb=" O PHE N 962 " (cutoff:3.500A) Processing helix chain 'N' and resid 1179 through 1187 Processing helix chain 'N' and resid 1205 through 1226 Processing helix chain 'N' and resid 1276 through 1289 Processing helix chain 'N' and resid 1295 through 1306 removed outlier: 4.023A pdb=" N LEU N1299 " --> pdb=" O LYS N1295 " (cutoff:3.500A) Processing helix chain 'N' and resid 1311 through 1325 Processing helix chain 'O' and resid 618 through 628 removed outlier: 3.612A pdb=" N LEU O 622 " --> pdb=" O CYS O 618 " (cutoff:3.500A) Processing helix chain 'O' and resid 633 through 650 Proline residue: O 644 - end of helix Processing helix chain 'O' and resid 675 through 684 removed outlier: 3.535A pdb=" N GLN O 679 " --> pdb=" O PRO O 675 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG O 684 " --> pdb=" O GLY O 680 " (cutoff:3.500A) Processing helix chain 'O' and resid 746 through 762 Processing helix chain 'O' and resid 768 through 788 removed outlier: 4.020A pdb=" N LEU O 772 " --> pdb=" O SER O 768 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA O 787 " --> pdb=" O ALA O 783 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 59 Processing helix chain 'P' and resid 147 through 150 Processing helix chain 'P' and resid 154 through 158 Processing helix chain 'P' and resid 364 through 374 Processing helix chain 'P' and resid 466 through 484 Processing helix chain 'P' and resid 488 through 493 Processing helix chain 'P' and resid 496 through 498 No H-bonds generated for 'chain 'P' and resid 496 through 498' Processing helix chain 'P' and resid 499 through 512 Processing helix chain 'P' and resid 517 through 522 Processing helix chain 'P' and resid 522 through 535 Processing helix chain 'P' and resid 540 through 542 No H-bonds generated for 'chain 'P' and resid 540 through 542' Processing helix chain 'P' and resid 543 through 564 removed outlier: 3.997A pdb=" N THR P 559 " --> pdb=" O ALA P 555 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU P 564 " --> pdb=" O LEU P 560 " (cutoff:3.500A) Processing helix chain 'P' and resid 575 through 587 Processing helix chain 'P' and resid 591 through 598 removed outlier: 3.821A pdb=" N VAL P 595 " --> pdb=" O ASP P 591 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN P 598 " --> pdb=" O LYS P 594 " (cutoff:3.500A) Processing helix chain 'P' and resid 609 through 614 Processing helix chain 'P' and resid 614 through 632 Processing helix chain 'P' and resid 648 through 669 Processing helix chain 'P' and resid 670 through 673 removed outlier: 3.726A pdb=" N LEU P 673 " --> pdb=" O PRO P 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 670 through 673' Processing helix chain 'P' and resid 684 through 701 removed outlier: 4.136A pdb=" N CYS P 699 " --> pdb=" O LYS P 695 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS P 700 " --> pdb=" O LEU P 696 " (cutoff:3.500A) Processing helix chain 'P' and resid 710 through 719 Processing helix chain 'P' and resid 719 through 724 Processing helix chain 'P' and resid 737 through 742 removed outlier: 3.936A pdb=" N ARG P 741 " --> pdb=" O GLY P 737 " (cutoff:3.500A) Processing helix chain 'P' and resid 816 through 821 Processing helix chain 'Q' and resid 36 through 47 removed outlier: 3.644A pdb=" N LEU Q 40 " --> pdb=" O MET Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 121 Processing helix chain 'Q' and resid 139 through 172 removed outlier: 3.591A pdb=" N THR Q 143 " --> pdb=" O GLN Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 194 Processing helix chain 'Q' and resid 290 through 318 removed outlier: 3.779A pdb=" N LYS Q 294 " --> pdb=" O HIS Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 387 removed outlier: 3.941A pdb=" N GLU Q 372 " --> pdb=" O LEU Q 368 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR Q 386 " --> pdb=" O PHE Q 382 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU Q 387 " --> pdb=" O HIS Q 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 388 through 392 removed outlier: 3.710A pdb=" N MET Q 391 " --> pdb=" O SER Q 388 " (cutoff:3.500A) Processing helix chain 'Q' and resid 402 through 408 Processing helix chain 'Q' and resid 414 through 422 removed outlier: 3.541A pdb=" N ILE Q 418 " --> pdb=" O ASP Q 414 " (cutoff:3.500A) Processing helix chain 'Q' and resid 426 through 455 removed outlier: 3.575A pdb=" N LYS Q 430 " --> pdb=" O GLY Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 519 through 544 removed outlier: 3.923A pdb=" N VAL Q 534 " --> pdb=" O SER Q 530 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL Q 537 " --> pdb=" O GLN Q 533 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL Q 543 " --> pdb=" O GLN Q 539 " (cutoff:3.500A) Processing helix chain 'Q' and resid 613 through 617 Processing helix chain 'Q' and resid 635 through 646 Processing helix chain 'R' and resid 28 through 43 removed outlier: 4.485A pdb=" N GLU R 33 " --> pdb=" O ASP R 29 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N SER R 34 " --> pdb=" O HIS R 30 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU R 35 " --> pdb=" O SER R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 122 removed outlier: 3.539A pdb=" N GLY R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 192 Processing helix chain 'S' and resid 82 through 87 Processing helix chain 'S' and resid 89 through 97 Processing helix chain 'S' and resid 112 through 117 Processing helix chain 'S' and resid 128 through 139 Proline residue: S 134 - end of helix Processing helix chain 'S' and resid 147 through 153 Processing helix chain 'T' and resid 16 through 32 Processing helix chain 'T' and resid 90 through 99 Processing helix chain 'T' and resid 153 through 165 Processing helix chain 'T' and resid 173 through 178 removed outlier: 3.654A pdb=" N ASN T 178 " --> pdb=" O ALA T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 204 removed outlier: 4.107A pdb=" N THR T 189 " --> pdb=" O GLY T 185 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET T 190 " --> pdb=" O PRO T 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 29 Processing helix chain 'U' and resid 49 through 76 Processing helix chain 'U' and resid 82 through 133 Processing helix chain 'V' and resid 11 through 40 Processing helix chain 'V' and resid 49 through 90 Processing helix chain 'V' and resid 90 through 136 removed outlier: 3.689A pdb=" N VAL V 94 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 13 removed outlier: 3.635A pdb=" N VAL W 13 " --> pdb=" O PHE W 9 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 51 Processing helix chain 'W' and resid 57 through 69 Processing helix chain 'W' and resid 72 through 89 Processing helix chain 'W' and resid 95 through 103 Processing helix chain 'W' and resid 111 through 126 Processing helix chain 'W' and resid 127 through 129 No H-bonds generated for 'chain 'W' and resid 127 through 129' Processing helix chain 'W' and resid 130 through 146 Processing helix chain 'W' and resid 156 through 161 Processing helix chain 'W' and resid 161 through 171 removed outlier: 3.709A pdb=" N GLU W 165 " --> pdb=" O LEU W 161 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL W 166 " --> pdb=" O ALA W 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 191 removed outlier: 3.587A pdb=" N ALA W 183 " --> pdb=" O PRO W 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 211 removed outlier: 4.202A pdb=" N PHE W 208 " --> pdb=" O LEU W 204 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 219 removed outlier: 3.565A pdb=" N ALA W 216 " --> pdb=" O PHE W 212 " (cutoff:3.500A) Processing helix chain 'W' and resid 223 through 227 removed outlier: 3.715A pdb=" N LEU W 227 " --> pdb=" O ARG W 224 " (cutoff:3.500A) Processing helix chain 'W' and resid 259 through 264 Processing helix chain 'W' and resid 266 through 275 removed outlier: 3.841A pdb=" N LEU W 270 " --> pdb=" O GLN W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 288 Processing helix chain 'W' and resid 297 through 318 removed outlier: 4.518A pdb=" N GLU W 318 " --> pdb=" O ARG W 314 " (cutoff:3.500A) Processing helix chain 'W' and resid 326 through 344 Processing helix chain 'W' and resid 348 through 361 removed outlier: 3.669A pdb=" N MET W 352 " --> pdb=" O SER W 348 " (cutoff:3.500A) Processing helix chain 'W' and resid 368 through 384 removed outlier: 3.570A pdb=" N LEU W 372 " --> pdb=" O GLY W 368 " (cutoff:3.500A) Processing helix chain 'W' and resid 388 through 393 removed outlier: 4.134A pdb=" N PHE W 392 " --> pdb=" O ALA W 388 " (cutoff:3.500A) Processing helix chain 'W' and resid 394 through 403 removed outlier: 3.844A pdb=" N LEU W 398 " --> pdb=" O PRO W 394 " (cutoff:3.500A) Processing helix chain 'W' and resid 418 through 423 Processing helix chain 'W' and resid 423 through 437 Processing helix chain 'W' and resid 451 through 464 Processing helix chain 'W' and resid 472 through 481 Processing helix chain 'W' and resid 488 through 501 removed outlier: 3.901A pdb=" N ALA W 494 " --> pdb=" O LEU W 490 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR W 498 " --> pdb=" O ALA W 494 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE W 499 " --> pdb=" O LEU W 495 " (cutoff:3.500A) Processing helix chain 'W' and resid 524 through 530 Processing helix chain 'W' and resid 532 through 553 Processing helix chain 'W' and resid 560 through 571 Processing helix chain 'W' and resid 573 through 579 removed outlier: 3.640A pdb=" N ILE W 576 " --> pdb=" O TYR W 573 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU W 577 " --> pdb=" O MET W 574 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N SER W 578 " --> pdb=" O GLU W 575 " (cutoff:3.500A) Processing helix chain 'W' and resid 580 through 587 Processing helix chain 'W' and resid 587 through 595 Processing helix chain 'W' and resid 599 through 611 Processing helix chain 'W' and resid 616 through 633 Processing helix chain 'W' and resid 638 through 654 Processing helix chain 'W' and resid 660 through 666 Processing helix chain 'W' and resid 671 through 676 removed outlier: 3.574A pdb=" N THR W 674 " --> pdb=" O ASP W 671 " (cutoff:3.500A) Processing helix chain 'W' and resid 680 through 698 removed outlier: 4.151A pdb=" N ASN W 684 " --> pdb=" O SER W 680 " (cutoff:3.500A) Processing helix chain 'W' and resid 710 through 721 removed outlier: 4.375A pdb=" N ASP W 714 " --> pdb=" O THR W 710 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE W 715 " --> pdb=" O TRP W 711 " (cutoff:3.500A) Processing helix chain 'W' and resid 728 through 733 Processing helix chain 'W' and resid 736 through 745 removed outlier: 3.945A pdb=" N GLN W 745 " --> pdb=" O ALA W 741 " (cutoff:3.500A) Processing helix chain 'W' and resid 752 through 770 Processing helix chain 'W' and resid 772 through 781 removed outlier: 3.623A pdb=" N SER W 781 " --> pdb=" O ILE W 777 " (cutoff:3.500A) Processing helix chain 'W' and resid 788 through 800 removed outlier: 3.755A pdb=" N GLU W 799 " --> pdb=" O LYS W 795 " (cutoff:3.500A) Processing helix chain 'W' and resid 805 through 815 removed outlier: 3.861A pdb=" N ARG W 809 " --> pdb=" O GLN W 805 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY W 815 " --> pdb=" O LEU W 811 " (cutoff:3.500A) Processing helix chain 'W' and resid 815 through 837 removed outlier: 3.605A pdb=" N LEU W 819 " --> pdb=" O GLY W 815 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL W 820 " --> pdb=" O ALA W 816 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA W 821 " --> pdb=" O ARG W 817 " (cutoff:3.500A) Processing helix chain 'W' and resid 840 through 855 Processing helix chain 'W' and resid 861 through 871 Processing helix chain 'W' and resid 876 through 892 Processing helix chain 'W' and resid 896 through 906 removed outlier: 3.652A pdb=" N GLU W 906 " --> pdb=" O ASP W 902 " (cutoff:3.500A) Processing helix chain 'W' and resid 916 through 928 removed outlier: 3.752A pdb=" N LYS W 920 " --> pdb=" O ASP W 916 " (cutoff:3.500A) Processing helix chain 'W' and resid 934 through 941 Processing helix chain 'W' and resid 959 through 977 removed outlier: 3.872A pdb=" N LEU W 964 " --> pdb=" O CYS W 960 " (cutoff:3.500A) Proline residue: W 965 - end of helix Processing helix chain 'W' and resid 980 through 991 removed outlier: 3.671A pdb=" N LEU W 984 " --> pdb=" O VAL W 980 " (cutoff:3.500A) Processing helix chain 'W' and resid 992 through 998 Processing helix chain 'W' and resid 1000 through 1012 Processing helix chain 'W' and resid 1019 through 1033 removed outlier: 3.557A pdb=" N LYS W1023 " --> pdb=" O ARG W1019 " (cutoff:3.500A) Processing helix chain 'W' and resid 1045 through 1052 removed outlier: 3.543A pdb=" N CYS W1051 " --> pdb=" O THR W1047 " (cutoff:3.500A) Processing helix chain 'W' and resid 1064 through 1081 removed outlier: 3.698A pdb=" N TYR W1068 " --> pdb=" O ASP W1064 " (cutoff:3.500A) Processing helix chain 'W' and resid 1091 through 1095 removed outlier: 3.818A pdb=" N ASN W1095 " --> pdb=" O TRP W1092 " (cutoff:3.500A) Processing helix chain 'W' and resid 1099 through 1114 removed outlier: 3.631A pdb=" N HIS W1103 " --> pdb=" O ASN W1099 " (cutoff:3.500A) Processing helix chain 'W' and resid 1118 through 1131 removed outlier: 4.220A pdb=" N VAL W1130 " --> pdb=" O LEU W1126 " (cutoff:3.500A) Processing helix chain 'W' and resid 1141 through 1155 removed outlier: 3.750A pdb=" N TRP W1145 " --> pdb=" O ASN W1141 " (cutoff:3.500A) Processing helix chain 'W' and resid 1157 through 1162 removed outlier: 3.573A pdb=" N TRP W1161 " --> pdb=" O PRO W1157 " (cutoff:3.500A) Processing helix chain 'W' and resid 1162 through 1173 removed outlier: 4.052A pdb=" N ASP W1166 " --> pdb=" O ILE W1162 " (cutoff:3.500A) Processing helix chain 'W' and resid 1186 through 1191 Processing helix chain 'W' and resid 1192 through 1198 Processing helix chain 'W' and resid 1203 through 1218 removed outlier: 3.707A pdb=" N HIS W1218 " --> pdb=" O ALA W1214 " (cutoff:3.500A) Processing helix chain 'W' and resid 1220 through 1225 Processing helix chain 'W' and resid 1226 through 1234 Processing helix chain 'W' and resid 1241 through 1253 Processing helix chain 'W' and resid 1255 through 1263 Processing helix chain 'W' and resid 1263 through 1284 removed outlier: 4.114A pdb=" N MET W1267 " --> pdb=" O ARG W1263 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE W1268 " --> pdb=" O THR W1264 " (cutoff:3.500A) Processing helix chain 'W' and resid 1290 through 1305 removed outlier: 3.556A pdb=" N ILE W1294 " --> pdb=" O TYR W1290 " (cutoff:3.500A) Processing helix chain 'W' and resid 1311 through 1320 removed outlier: 3.645A pdb=" N GLU W1315 " --> pdb=" O LYS W1311 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS W1316 " --> pdb=" O GLU W1312 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE W1317 " --> pdb=" O GLN W1313 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN W1320 " --> pdb=" O LYS W1316 " (cutoff:3.500A) Processing helix chain 'W' and resid 1322 through 1330 Processing helix chain 'W' and resid 1331 through 1334 removed outlier: 3.624A pdb=" N HIS W1334 " --> pdb=" O PHE W1331 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 1331 through 1334' Processing helix chain 'X' and resid 5 through 16 Processing helix chain 'X' and resid 19 through 31 Processing helix chain 'X' and resid 34 through 38 removed outlier: 3.580A pdb=" N ASP X 38 " --> pdb=" O ALA X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 49 Processing helix chain 'X' and resid 57 through 70 Processing helix chain 'X' and resid 74 through 84 removed outlier: 3.547A pdb=" N VAL X 78 " --> pdb=" O SER X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 105 removed outlier: 3.635A pdb=" N VAL X 94 " --> pdb=" O ARG X 90 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE X 104 " --> pdb=" O ILE X 100 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 146 Processing helix chain 'X' and resid 156 through 171 removed outlier: 4.112A pdb=" N SER X 171 " --> pdb=" O LYS X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 171 through 185 removed outlier: 4.247A pdb=" N LEU X 183 " --> pdb=" O HIS X 179 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU X 184 " --> pdb=" O ILE X 180 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU X 185 " --> pdb=" O ALA X 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 206 removed outlier: 3.743A pdb=" N ALA X 191 " --> pdb=" O SER X 187 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU X 206 " --> pdb=" O ILE X 202 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 225 Processing helix chain 'X' and resid 241 through 254 removed outlier: 3.736A pdb=" N HIS X 245 " --> pdb=" O PHE X 241 " (cutoff:3.500A) Processing helix chain 'X' and resid 259 through 274 removed outlier: 3.736A pdb=" N LEU X 263 " --> pdb=" O GLU X 259 " (cutoff:3.500A) Processing helix chain 'X' and resid 277 through 295 Processing helix chain 'X' and resid 299 through 311 removed outlier: 3.561A pdb=" N LEU X 303 " --> pdb=" O GLY X 299 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 324 Processing helix chain 'X' and resid 330 through 343 Processing helix chain 'X' and resid 344 through 356 Processing helix chain 'X' and resid 358 through 370 removed outlier: 3.990A pdb=" N PHE X 362 " --> pdb=" O ASP X 358 " (cutoff:3.500A) Processing helix chain 'X' and resid 374 through 391 removed outlier: 4.085A pdb=" N HIS X 391 " --> pdb=" O ALA X 387 " (cutoff:3.500A) Processing helix chain 'X' and resid 405 through 424 Proline residue: X 415 - end of helix Processing helix chain 'X' and resid 426 through 431 Processing helix chain 'X' and resid 431 through 444 Processing helix chain 'X' and resid 446 through 458 Processing helix chain 'X' and resid 460 through 478 removed outlier: 4.614A pdb=" N TYR X 477 " --> pdb=" O GLU X 473 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY X 478 " --> pdb=" O PHE X 474 " (cutoff:3.500A) Processing helix chain 'X' and resid 482 through 507 removed outlier: 3.974A pdb=" N LEU X 491 " --> pdb=" O SER X 487 " (cutoff:3.500A) Processing helix chain 'X' and resid 523 through 533 removed outlier: 3.516A pdb=" N THR X 527 " --> pdb=" O PRO X 523 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET X 533 " --> pdb=" O MET X 529 " (cutoff:3.500A) Processing helix chain 'X' and resid 544 through 548 Processing helix chain 'X' and resid 551 through 562 removed outlier: 3.731A pdb=" N GLU X 555 " --> pdb=" O SER X 551 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER X 556 " --> pdb=" O THR X 552 " (cutoff:3.500A) Processing helix chain 'X' and resid 573 through 595 removed outlier: 4.880A pdb=" N SER X 582 " --> pdb=" O CYS X 578 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA X 583 " --> pdb=" O LEU X 579 " (cutoff:3.500A) Processing helix chain 'X' and resid 598 through 611 Processing helix chain 'X' and resid 614 through 631 Processing helix chain 'X' and resid 636 through 647 removed outlier: 3.902A pdb=" N GLN X 641 " --> pdb=" O GLU X 637 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET X 642 " --> pdb=" O LYS X 638 " (cutoff:3.500A) Processing helix chain 'X' and resid 658 through 675 Processing helix chain 'X' and resid 676 through 681 removed outlier: 3.516A pdb=" N THR X 681 " --> pdb=" O VAL X 677 " (cutoff:3.500A) Processing helix chain 'X' and resid 706 through 722 removed outlier: 3.835A pdb=" N VAL X 710 " --> pdb=" O PRO X 706 " (cutoff:3.500A) Processing helix chain 'X' and resid 725 through 754 removed outlier: 3.527A pdb=" N ILE X 729 " --> pdb=" O ASP X 725 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL X 741 " --> pdb=" O HIS X 737 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N TYR X 742 " --> pdb=" O MET X 738 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP X 743 " --> pdb=" O GLY X 739 " (cutoff:3.500A) Processing helix chain 'X' and resid 757 through 773 removed outlier: 4.223A pdb=" N SER X 770 " --> pdb=" O GLU X 766 " (cutoff:3.500A) Processing helix chain 'X' and resid 775 through 786 Processing helix chain 'X' and resid 786 through 794 Processing helix chain 'X' and resid 796 through 801 removed outlier: 4.115A pdb=" N HIS X 799 " --> pdb=" O SER X 796 " (cutoff:3.500A) Processing helix chain 'X' and resid 802 through 823 removed outlier: 4.030A pdb=" N ALA X 808 " --> pdb=" O PRO X 804 " (cutoff:3.500A) Processing helix chain 'X' and resid 829 through 839 Processing helix chain 'X' and resid 842 through 847 Processing helix chain 'X' and resid 895 through 914 removed outlier: 3.538A pdb=" N ARG X 899 " --> pdb=" O ASP X 895 " (cutoff:3.500A) Processing helix chain 'X' and resid 918 through 935 removed outlier: 3.532A pdb=" N GLN X 922 " --> pdb=" O GLY X 918 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU X 935 " --> pdb=" O CYS X 931 " (cutoff:3.500A) Processing helix chain 'X' and resid 942 through 947 Processing helix chain 'X' and resid 949 through 958 removed outlier: 4.020A pdb=" N SER X 953 " --> pdb=" O PHE X 949 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL X 956 " --> pdb=" O VAL X 952 " (cutoff:3.500A) Processing helix chain 'X' and resid 966 through 970 Processing helix chain 'X' and resid 975 through 988 removed outlier: 4.075A pdb=" N GLN X 980 " --> pdb=" O PRO X 976 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 39 Processing helix chain 'Y' and resid 39 through 48 Processing helix chain 'Y' and resid 90 through 101 removed outlier: 3.509A pdb=" N PHE Y 94 " --> pdb=" O SER Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 132 removed outlier: 3.561A pdb=" N GLY Y 117 " --> pdb=" O LEU Y 113 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 175 Processing helix chain 'Y' and resid 176 through 178 No H-bonds generated for 'chain 'Y' and resid 176 through 178' Processing helix chain 'Y' and resid 188 through 198 removed outlier: 3.695A pdb=" N ARG Y 192 " --> pdb=" O LEU Y 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 484 through 500 Processing helix chain 'Z' and resid 549 through 557 Processing helix chain '0' and resid 8 through 38 removed outlier: 3.613A pdb=" N GLY 0 38 " --> pdb=" O CYS 0 34 " (cutoff:3.500A) Processing helix chain '0' and resid 44 through 77 Processing helix chain '0' and resid 104 through 131 removed outlier: 3.696A pdb=" N GLN 0 131 " --> pdb=" O LEU 0 127 " (cutoff:3.500A) Processing helix chain '0' and resid 158 through 172 removed outlier: 3.569A pdb=" N VAL 0 162 " --> pdb=" O PRO 0 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET 0 172 " --> pdb=" O ARG 0 168 " (cutoff:3.500A) Processing helix chain '0' and resid 236 through 253 removed outlier: 3.645A pdb=" N GLN 0 240 " --> pdb=" O TYR 0 236 " (cutoff:3.500A) Processing helix chain '0' and resid 259 through 272 removed outlier: 3.740A pdb=" N SER 0 272 " --> pdb=" O THR 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 273 through 276 Processing helix chain '0' and resid 306 through 310 Processing helix chain '1' and resid 43 through 56 removed outlier: 3.709A pdb=" N GLU 1 47 " --> pdb=" O THR 1 43 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE 1 56 " --> pdb=" O PHE 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 106 Processing helix chain '1' and resid 107 through 144 Processing helix chain '2' and resid 56 through 90 Proline residue: 2 65 - end of helix Processing helix chain '2' and resid 101 through 136 removed outlier: 4.238A pdb=" N CYS 2 105 " --> pdb=" O ARG 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 156 through 186 removed outlier: 4.328A pdb=" N THR 2 186 " --> pdb=" O ALA 2 182 " (cutoff:3.500A) Processing helix chain '3' and resid 30 through 58 removed outlier: 4.529A pdb=" N ARG 3 35 " --> pdb=" O ALA 3 31 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR 3 46 " --> pdb=" O GLN 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 70 through 102 Processing helix chain '3' and resid 137 through 176 Processing helix chain '4' and resid 11 through 29 Processing helix chain '4' and resid 30 through 40 Processing helix chain '4' and resid 45 through 55 removed outlier: 3.674A pdb=" N VAL 4 49 " --> pdb=" O ASP 4 45 " (cutoff:3.500A) Processing helix chain '4' and resid 56 through 59 Processing helix chain '4' and resid 60 through 65 Processing helix chain '4' and resid 71 through 80 Processing helix chain '4' and resid 82 through 87 removed outlier: 3.600A pdb=" N LYS 4 86 " --> pdb=" O GLU 4 82 " (cutoff:3.500A) Processing helix chain '4' and resid 90 through 106 removed outlier: 3.619A pdb=" N ALA 4 94 " --> pdb=" O ASN 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 106 through 122 removed outlier: 3.820A pdb=" N GLN 4 122 " --> pdb=" O ALA 4 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 212 removed outlier: 3.665A pdb=" N TYR A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN A 221 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 257 " --> pdb=" O ASN A 221 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS A 223 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA A 255 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 225 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ASN A 254 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER A 394 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N GLN A 309 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N LEU A 392 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N ILE A 311 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N GLY A 390 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 269 removed outlier: 3.503A pdb=" N VAL A 297 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 362 through 366 removed outlier: 7.176A pdb=" N GLN A 371 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE A 440 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS A 373 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL A 442 " --> pdb=" O CYS A 373 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE A 375 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLN A 439 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN A 455 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 445 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 143 through 144 Processing sheet with id=AA6, first strand: chain 'F' and resid 66 through 73 removed outlier: 6.326A pdb=" N ILE F 80 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE F 79 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLN F 85 " --> pdb=" O PRO F 94 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLN F 87 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL F 92 " --> pdb=" O GLN F 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 137 through 140 Processing sheet with id=AA8, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AA9, first strand: chain 'N' and resid 224 through 226 removed outlier: 3.625A pdb=" N PHE N 230 " --> pdb=" O VAL N 226 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS N 249 " --> pdb=" O THR N 233 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR N 235 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU N 247 " --> pdb=" O THR N 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 324 through 330 removed outlier: 6.645A pdb=" N SER N 336 " --> pdb=" O GLU N 327 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR N 329 " --> pdb=" O CYS N 334 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS N 334 " --> pdb=" O TYR N 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 430 through 432 Processing sheet with id=AB3, first strand: chain 'N' and resid 514 through 517 removed outlier: 5.269A pdb=" N TYR N 548 " --> pdb=" O LEU N 542 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER N 572 " --> pdb=" O LEU N 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 682 through 683 removed outlier: 5.296A pdb=" N LEU N 705 " --> pdb=" O ALA N 727 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ALA N 727 " --> pdb=" O LEU N 705 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP N 707 " --> pdb=" O VAL N 725 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR N 709 " --> pdb=" O GLU N 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 798 through 803 removed outlier: 5.327A pdb=" N VAL N 800 " --> pdb=" O CYS N 811 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS N 811 " --> pdb=" O VAL N 800 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 904 through 908 removed outlier: 4.241A pdb=" N VAL N 933 " --> pdb=" O ARG N 929 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 1240 through 1242 Processing sheet with id=AB8, first strand: chain 'N' and resid 1338 through 1339 Processing sheet with id=AB9, first strand: chain 'O' and resid 692 through 693 removed outlier: 4.441A pdb=" N GLU O 722 " --> pdb=" O ILE O 737 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 431 through 436 removed outlier: 6.489A pdb=" N ILE P 446 " --> pdb=" O LYS P 432 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET P 434 " --> pdb=" O VAL P 444 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL P 444 " --> pdb=" O MET P 434 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU P 436 " --> pdb=" O ALA P 442 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA P 442 " --> pdb=" O LEU P 436 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR P 17 " --> pdb=" O VAL P 454 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG P 456 " --> pdb=" O LEU P 15 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU P 15 " --> pdb=" O ARG P 456 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 37 through 39 Processing sheet with id=AC3, first strand: chain 'P' and resid 84 through 89 removed outlier: 6.443A pdb=" N ILE P 105 " --> pdb=" O GLY P 123 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY P 123 " --> pdb=" O ILE P 105 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N CYS P 107 " --> pdb=" O SER P 121 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER P 121 " --> pdb=" O CYS P 107 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER P 117 " --> pdb=" O ALA P 111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 131 through 136 removed outlier: 6.454A pdb=" N VAL P 182 " --> pdb=" O VAL P 132 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU P 134 " --> pdb=" O ILE P 180 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE P 180 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TRP P 136 " --> pdb=" O GLY P 178 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY P 178 " --> pdb=" O TRP P 136 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU P 177 " --> pdb=" O LEU P 193 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU P 187 " --> pdb=" O THR P 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 143 through 145 Processing sheet with id=AC6, first strand: chain 'P' and resid 215 through 220 Processing sheet with id=AC7, first strand: chain 'P' and resid 279 through 287 removed outlier: 5.182A pdb=" N ILE P 280 " --> pdb=" O SER P 299 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER P 299 " --> pdb=" O ILE P 280 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS P 282 " --> pdb=" O CYS P 297 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLN P 293 " --> pdb=" O LEU P 286 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL P 306 " --> pdb=" O ALA P 344 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA P 344 " --> pdb=" O VAL P 306 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS P 308 " --> pdb=" O LEU P 342 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 351 through 355 removed outlier: 4.111A pdb=" N ALA P 353 " --> pdb=" O ALA P 385 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL P 391 " --> pdb=" O VAL P 404 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL P 404 " --> pdb=" O VAL P 391 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE P 393 " --> pdb=" O MET P 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 804 through 806 removed outlier: 4.549A pdb=" N CYS P 795 " --> pdb=" O VAL P 836 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 195 through 199 removed outlier: 4.555A pdb=" N LYS Q 195 " --> pdb=" O ASP Q 206 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE Q 203 " --> pdb=" O VAL Q 224 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 255 through 262 Processing sheet with id=AD3, first strand: chain 'Q' and resid 461 through 462 Processing sheet with id=AD4, first strand: chain 'Q' and resid 461 through 462 removed outlier: 3.767A pdb=" N ILE Q 502 " --> pdb=" O LEU Q 514 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 547 through 555 removed outlier: 6.824A pdb=" N LEU Q 549 " --> pdb=" O ALA Q 572 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA Q 572 " --> pdb=" O LEU Q 549 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE Q 551 " --> pdb=" O THR Q 570 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR Q 570 " --> pdb=" O PHE Q 551 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN Q 553 " --> pdb=" O ALA Q 568 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ALA Q 568 " --> pdb=" O ASN Q 553 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA Q 566 " --> pdb=" O VAL Q 555 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR Q 578 " --> pdb=" O SER Q 573 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 160 through 162 removed outlier: 4.325A pdb=" N MET R 18 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU R 88 " --> pdb=" O VAL R 69 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL R 69 " --> pdb=" O LEU R 88 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS R 127 " --> pdb=" O VAL R 57 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU R 59 " --> pdb=" O MET R 125 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N MET R 125 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU R 128 " --> pdb=" O ILE R 151 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE R 151 " --> pdb=" O GLU R 128 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 3 through 9 removed outlier: 3.897A pdb=" N ILE T 138 " --> pdb=" O MET T 9 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER T 134 " --> pdb=" O MET T 131 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL T 129 " --> pdb=" O ARG T 136 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE T 138 " --> pdb=" O GLY T 127 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLY T 127 " --> pdb=" O ILE T 138 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL T 140 " --> pdb=" O LYS T 125 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS T 125 " --> pdb=" O VAL T 140 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL T 142 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU T 123 " --> pdb=" O VAL T 142 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL T 126 " --> pdb=" O THR T 115 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR T 115 " --> pdb=" O VAL T 126 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG T 113 " --> pdb=" O THR T 128 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU T 111 " --> pdb=" O THR T 130 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY T 37 " --> pdb=" O ARG T 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLN T 118 " --> pdb=" O LYS T 35 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LYS T 35 " --> pdb=" O GLN T 118 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 506 through 507 removed outlier: 7.013A pdb=" N MET W 515 " --> pdb=" O ALA W 558 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 83 through 84 removed outlier: 6.038A pdb=" N ASP Y 17 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU Y 143 " --> pdb=" O ASP Y 17 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL Y 19 " --> pdb=" O LEU Y 143 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE Y 145 " --> pdb=" O VAL Y 19 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL Y 21 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 565 through 566 Processing sheet with id=AE2, first strand: chain 'Z' and resid 580 through 582 Processing sheet with id=AE3, first strand: chain '0' and resid 176 through 181 Processing sheet with id=AE4, first strand: chain '0' and resid 296 through 297 3673 hydrogen bonds defined for protein. 10713 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: 28.30 Time building geometry restraints manager: 13.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 10377 1.31 - 1.44: 16189 1.44 - 1.57: 36402 1.57 - 1.70: 0 1.70 - 1.83: 604 Bond restraints: 63572 Sorted by residual: bond pdb=" C VAL O 643 " pdb=" N PRO O 644 " ideal model delta sigma weight residual 1.336 1.394 -0.059 1.23e-02 6.61e+03 2.28e+01 bond pdb=" C PRO X 432 " pdb=" O PRO X 432 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.16e-02 7.43e+03 2.00e+01 bond pdb=" N VAL T 148 " pdb=" CA VAL T 148 " ideal model delta sigma weight residual 1.459 1.496 -0.037 9.10e-03 1.21e+04 1.67e+01 bond pdb=" N ILE A 270 " pdb=" CA ILE A 270 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.09e-02 8.42e+03 1.66e+01 bond pdb=" N LEU U 76 " pdb=" CA LEU U 76 " ideal model delta sigma weight residual 1.457 1.514 -0.057 1.41e-02 5.03e+03 1.63e+01 ... (remaining 63567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 82699 2.65 - 5.30: 2939 5.30 - 7.96: 360 7.96 - 10.61: 96 10.61 - 13.26: 12 Bond angle restraints: 86106 Sorted by residual: angle pdb=" N PRO N1351 " pdb=" CA PRO N1351 " pdb=" CB PRO N1351 " ideal model delta sigma weight residual 103.08 112.14 -9.06 9.70e-01 1.06e+00 8.72e+01 angle pdb=" N PRO N1343 " pdb=" CA PRO N1343 " pdb=" CB PRO N1343 " ideal model delta sigma weight residual 103.08 112.06 -8.98 9.70e-01 1.06e+00 8.56e+01 angle pdb=" N HIS 4 83 " pdb=" CA HIS 4 83 " pdb=" C HIS 4 83 " ideal model delta sigma weight residual 112.90 100.97 11.93 1.31e+00 5.83e-01 8.29e+01 angle pdb=" N GLN F 173 " pdb=" CA GLN F 173 " pdb=" C GLN F 173 " ideal model delta sigma weight residual 112.94 100.92 12.02 1.41e+00 5.03e-01 7.27e+01 angle pdb=" N PRO N1355 " pdb=" CA PRO N1355 " pdb=" CB PRO N1355 " ideal model delta sigma weight residual 103.25 111.56 -8.31 1.05e+00 9.07e-01 6.26e+01 ... (remaining 86101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 34222 17.99 - 35.98: 3715 35.98 - 53.97: 673 53.97 - 71.96: 101 71.96 - 89.95: 42 Dihedral angle restraints: 38753 sinusoidal: 15553 harmonic: 23200 Sorted by residual: dihedral pdb=" C PHE X 310 " pdb=" N PHE X 310 " pdb=" CA PHE X 310 " pdb=" CB PHE X 310 " ideal model delta harmonic sigma weight residual -122.60 -141.16 18.56 0 2.50e+00 1.60e-01 5.51e+01 dihedral pdb=" C TYR 4 81 " pdb=" N TYR 4 81 " pdb=" CA TYR 4 81 " pdb=" CB TYR 4 81 " ideal model delta harmonic sigma weight residual -122.60 -139.16 16.56 0 2.50e+00 1.60e-01 4.39e+01 dihedral pdb=" N PHE X 310 " pdb=" C PHE X 310 " pdb=" CA PHE X 310 " pdb=" CB PHE X 310 " ideal model delta harmonic sigma weight residual 122.80 138.14 -15.34 0 2.50e+00 1.60e-01 3.76e+01 ... (remaining 38750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 9356 0.138 - 0.276: 487 0.276 - 0.414: 28 0.414 - 0.552: 5 0.552 - 0.690: 2 Chirality restraints: 9878 Sorted by residual: chirality pdb=" CA PHE X 310 " pdb=" N PHE X 310 " pdb=" C PHE X 310 " pdb=" CB PHE X 310 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA TYR 4 81 " pdb=" N TYR 4 81 " pdb=" C TYR 4 81 " pdb=" CB TYR 4 81 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" CA GLN T 204 " pdb=" N GLN T 204 " pdb=" C GLN T 204 " pdb=" CB GLN T 204 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.62e+00 ... (remaining 9875 not shown) Planarity restraints: 10995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG P 640 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO P 641 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO P 641 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO P 641 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 167 " -0.021 2.00e-02 2.50e+03 4.12e-02 1.69e+01 pdb=" C ASN A 167 " 0.071 2.00e-02 2.50e+03 pdb=" O ASN A 167 " -0.026 2.00e-02 2.50e+03 pdb=" N LYS A 168 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU X 975 " -0.061 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO X 976 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO X 976 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO X 976 " -0.050 5.00e-02 4.00e+02 ... (remaining 10992 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 8997 2.75 - 3.28: 60634 3.28 - 3.82: 103968 3.82 - 4.36: 120686 4.36 - 4.90: 207535 Nonbonded interactions: 501820 Sorted by model distance: nonbonded pdb=" O GLU Y 45 " pdb=" O ASN Y 48 " model vdw 2.207 3.040 nonbonded pdb=" O ASN W 726 " pdb=" OG SER W 873 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR W 764 " pdb=" OE2 GLU W 799 " model vdw 2.216 3.040 nonbonded pdb=" O GLY H 54 " pdb=" OG1 THR H 58 " model vdw 2.218 3.040 nonbonded pdb=" CD1 ILE G 18 " pdb=" OH TYR 4 51 " model vdw 2.223 3.460 ... (remaining 501815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 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: 5.660 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: 1.860 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 120.100 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.240 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: 0.030 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 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 : 0.011 0.106 63572 Z= 0.742 Angle : 1.171 13.260 86106 Z= 0.699 Chirality : 0.070 0.690 9878 Planarity : 0.009 0.105 10995 Dihedral : 15.265 89.949 23597 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.63 % Favored : 93.77 % Rotamer: Outliers : 1.08 % Allowed : 8.90 % Favored : 90.02 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.08), residues: 7758 helix: -1.08 (0.07), residues: 4210 sheet: -1.43 (0.16), residues: 842 loop : -2.81 (0.10), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP X 798 HIS 0.017 0.002 HIS Q 383 PHE 0.037 0.003 PHE N 152 TYR 0.026 0.003 TYR N 166 ARG 0.012 0.001 ARG P 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1441 time to evaluate : 5.368 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 77 MET cc_start: 0.1851 (mmp) cc_final: 0.1573 (ptm) REVERT: A 492 ASP cc_start: 0.7209 (m-30) cc_final: 0.6706 (m-30) REVERT: D 92 GLU cc_start: 0.4099 (tm-30) cc_final: 0.3412 (mt-10) REVERT: D 119 GLN cc_start: 0.4966 (tm-30) cc_final: 0.3485 (mt0) REVERT: F 174 ARG cc_start: 0.5630 (mmt180) cc_final: 0.4514 (ptt-90) REVERT: F 187 LYS cc_start: 0.6788 (ttmt) cc_final: 0.6527 (ttmm) REVERT: G 44 MET cc_start: 0.1000 (ttp) cc_final: -0.0562 (mpp) REVERT: G 70 MET cc_start: 0.3965 (mmm) cc_final: 0.3691 (mtt) REVERT: G 162 GLU cc_start: 0.2853 (pp20) cc_final: 0.2085 (tm-30) REVERT: I 76 MET cc_start: 0.3229 (tmm) cc_final: 0.2906 (mpp) REVERT: I 104 MET cc_start: 0.3190 (mmp) cc_final: 0.2598 (tmm) REVERT: I 121 LEU cc_start: 0.5137 (mt) cc_final: 0.4804 (tp) REVERT: K 114 MET cc_start: 0.8445 (ttt) cc_final: 0.8198 (ttp) REVERT: N 227 GLU cc_start: 0.6565 (mp0) cc_final: 0.6066 (mp0) REVERT: N 305 LEU cc_start: 0.8506 (mt) cc_final: 0.8031 (tt) REVERT: N 674 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7053 (tm-30) REVERT: N 703 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7526 (ttp-110) REVERT: N 795 ASN cc_start: 0.7713 (t0) cc_final: 0.7360 (t0) REVERT: N 799 GLU cc_start: 0.4879 (mm-30) cc_final: 0.4593 (mm-30) REVERT: N 841 ASN cc_start: 0.8175 (m-40) cc_final: 0.7935 (m-40) REVERT: N 870 GLN cc_start: 0.8315 (tp40) cc_final: 0.7589 (tt0) REVERT: N 924 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8025 (mp) REVERT: N 1286 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8068 (tm-30) REVERT: O 750 GLN cc_start: 0.7335 (mt0) cc_final: 0.6987 (mm-40) REVERT: P 30 CYS cc_start: 0.8779 (t) cc_final: 0.8384 (m) REVERT: P 90 ASP cc_start: 0.7759 (t0) cc_final: 0.7345 (t70) REVERT: P 163 LYS cc_start: 0.8475 (tptt) cc_final: 0.8071 (tptt) REVERT: P 369 LYS cc_start: 0.7934 (mttt) cc_final: 0.7640 (tppt) REVERT: P 447 ASP cc_start: 0.8132 (m-30) cc_final: 0.7853 (m-30) REVERT: P 471 LEU cc_start: 0.8006 (mm) cc_final: 0.7796 (mt) REVERT: P 472 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7833 (mtp180) REVERT: P 598 ASN cc_start: 0.8146 (m-40) cc_final: 0.7639 (t0) REVERT: P 754 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.8198 (tpt170) REVERT: P 825 LYS cc_start: 0.8685 (pttt) cc_final: 0.8402 (ptmt) REVERT: Q 250 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7868 (p0) REVERT: Q 264 GLN cc_start: 0.6200 (tm-30) cc_final: 0.5773 (mp10) REVERT: Q 328 LYS cc_start: 0.7596 (ptpt) cc_final: 0.7223 (pttt) REVERT: Q 643 MET cc_start: 0.9182 (mtt) cc_final: 0.8876 (mtt) REVERT: R 32 LEU cc_start: 0.3986 (OUTLIER) cc_final: 0.3665 (tp) REVERT: R 93 MET cc_start: 0.3140 (mmt) cc_final: 0.2784 (ptt) REVERT: R 119 MET cc_start: 0.7726 (mmm) cc_final: 0.7147 (ptt) REVERT: R 143 ILE cc_start: 0.6822 (mm) cc_final: 0.6368 (mt) REVERT: R 201 LYS cc_start: 0.5681 (ttpt) cc_final: 0.4731 (pptt) REVERT: T 1 MET cc_start: 0.6773 (ptp) cc_final: 0.6107 (ptp) REVERT: T 119 TYR cc_start: 0.8199 (t80) cc_final: 0.7997 (t80) REVERT: T 121 ASP cc_start: 0.7918 (m-30) cc_final: 0.7674 (m-30) REVERT: T 152 ASP cc_start: 0.7112 (m-30) cc_final: 0.6332 (t0) REVERT: V 98 ILE cc_start: 0.6003 (mt) cc_final: 0.5686 (mm) REVERT: V 103 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7729 (tm-30) REVERT: V 108 LEU cc_start: 0.8525 (tp) cc_final: 0.7897 (tp) REVERT: V 126 ASP cc_start: 0.7774 (m-30) cc_final: 0.7249 (m-30) REVERT: W 37 LEU cc_start: 0.8452 (mt) cc_final: 0.8190 (mt) REVERT: W 111 ARG cc_start: 0.8240 (mmm160) cc_final: 0.7980 (mtp180) REVERT: W 282 MET cc_start: 0.8333 (ttt) cc_final: 0.8017 (ttt) REVERT: W 310 TYR cc_start: 0.8533 (t80) cc_final: 0.8166 (t80) REVERT: W 338 LEU cc_start: 0.9242 (tp) cc_final: 0.8912 (tt) REVERT: W 354 LEU cc_start: 0.9025 (pp) cc_final: 0.8776 (pp) REVERT: W 396 MET cc_start: 0.8751 (mtt) cc_final: 0.8273 (mtp) REVERT: W 498 THR cc_start: 0.7721 (p) cc_final: 0.7393 (t) REVERT: W 646 GLU cc_start: 0.7550 (tt0) cc_final: 0.7300 (tm-30) REVERT: W 672 PRO cc_start: 0.7993 (Cg_endo) cc_final: 0.7738 (Cg_exo) REVERT: W 796 MET cc_start: 0.7961 (mtt) cc_final: 0.7531 (ttt) REVERT: W 811 LEU cc_start: 0.8242 (mt) cc_final: 0.7740 (mt) REVERT: W 1012 TYR cc_start: 0.8907 (m-80) cc_final: 0.8621 (m-80) REVERT: W 1277 MET cc_start: 0.8921 (mtt) cc_final: 0.8425 (mtp) REVERT: X 29 LYS cc_start: 0.8479 (mttt) cc_final: 0.7992 (ttpt) REVERT: X 183 LEU cc_start: 0.6786 (mp) cc_final: 0.6349 (tt) REVERT: X 222 ILE cc_start: 0.7186 (mt) cc_final: 0.6911 (mt) REVERT: X 223 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7548 (mmm160) REVERT: X 273 MET cc_start: 0.8429 (mmt) cc_final: 0.8053 (mtp) REVERT: X 604 LYS cc_start: 0.8198 (tmmt) cc_final: 0.7968 (tttm) REVERT: X 654 ASN cc_start: 0.7087 (m-40) cc_final: 0.6745 (t0) REVERT: X 837 ARG cc_start: 0.6721 (mtt180) cc_final: 0.6422 (ttm-80) REVERT: X 894 ARG cc_start: 0.8190 (mmm160) cc_final: 0.7802 (mtp-110) REVERT: Y 195 PHE cc_start: 0.7782 (t80) cc_final: 0.7423 (t80) REVERT: Y 220 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8535 (ttm) REVERT: Y 224 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7312 (mtt90) REVERT: 0 109 GLN cc_start: 0.7271 (tp40) cc_final: 0.7029 (tt0) REVERT: 0 160 GLN cc_start: 0.7807 (tp-100) cc_final: 0.7446 (tm-30) REVERT: 0 164 ASP cc_start: 0.7165 (m-30) cc_final: 0.6165 (m-30) REVERT: 0 229 ASP cc_start: 0.8997 (t0) cc_final: 0.8779 (t70) REVERT: 0 287 PHE cc_start: 0.8277 (m-80) cc_final: 0.7807 (m-80) REVERT: 0 307 ASP cc_start: 0.8325 (p0) cc_final: 0.7738 (t0) REVERT: 1 103 SER cc_start: 0.8948 (t) cc_final: 0.8705 (m) REVERT: 1 121 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7804 (mm-30) REVERT: 1 131 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8458 (ttmm) REVERT: 2 80 GLN cc_start: 0.8242 (mt0) cc_final: 0.7981 (mt0) REVERT: 2 89 ASP cc_start: 0.7918 (m-30) cc_final: 0.7686 (m-30) REVERT: 2 117 GLU cc_start: 0.8416 (tt0) cc_final: 0.8188 (tt0) REVERT: 3 46 TYR cc_start: 0.7643 (t80) cc_final: 0.7125 (t80) REVERT: 4 75 MET cc_start: 0.0932 (mmm) cc_final: -0.0160 (mtm) REVERT: 4 80 GLN cc_start: 0.2203 (OUTLIER) cc_final: 0.1734 (tp40) REVERT: 4 113 MET cc_start: 0.1876 (mmm) cc_final: 0.0817 (ptm) outliers start: 74 outliers final: 20 residues processed: 1497 average time/residue: 0.6256 time to fit residues: 1537.8281 Evaluate side-chains 766 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 740 time to evaluate : 5.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 72 PHE Chi-restraints excluded: chain I residue 105 PRO Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 725 VAL Chi-restraints excluded: chain N residue 924 ILE Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain Y residue 220 MET Chi-restraints excluded: chain Y residue 224 ARG Chi-restraints excluded: chain Z residue 482 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 207 LEU Chi-restraints excluded: chain 0 residue 218 ASN Chi-restraints excluded: chain 4 residue 80 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 659 optimal weight: 0.7980 chunk 591 optimal weight: 3.9990 chunk 328 optimal weight: 0.0370 chunk 202 optimal weight: 0.3980 chunk 399 optimal weight: 6.9990 chunk 316 optimal weight: 0.5980 chunk 612 optimal weight: 0.7980 chunk 236 optimal weight: 0.0270 chunk 372 optimal weight: 0.7980 chunk 455 optimal weight: 1.9990 chunk 709 optimal weight: 6.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 131 ASN A 221 ASN A 322 GLN A 359 HIS A 400 HIS A 413 HIS A 414 GLN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN F 46 ASN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 ASN G 142 GLN H 7 GLN H 18 GLN H 174 ASN ** K 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 GLN K 113 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 267 HIS N 309 HIS N 532 ASN N 590 GLN N 638 ASN N 669 GLN N 846 ASN N 849 ASN N 856 GLN N 964 ASN N1179 HIS O 679 GLN O 701 ASN O 742 GLN O 746 ASN P 63 HIS P 80 HIS P 113 HIS P 272 ASN P 282 HIS P 435 GLN ** P 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 619 GLN P 634 ASN Q 100 ASN Q 139 GLN Q 193 HIS Q 219 HIS Q 340 GLN Q 468 ASN Q 492 GLN Q 506 HIS Q 517 GLN Q 528 GLN Q 532 HIS Q 539 GLN Q 565 ASN R 97 ASN T 103 GLN T 162 GLN T 192 GLN T 205 GLN ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 ASN U 56 GLN U 119 GLN V 32 ASN ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 4 GLN W 293 HIS W 337 GLN W 357 HIS W 378 GLN ** W 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 513 ASN ** W 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 844 ASN W 851 ASN W 923 ASN W 972 HIS W 990 HIS W1059 ASN W1198 GLN W1261 GLN W1300 HIS W1320 ASN X 8 GLN X 49 GLN X 179 HIS X 217 GLN X 266 GLN X 361 ASN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 402 ASN ** X 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 472 ASN X 502 HIS X 544 HIS X 627 HIS X 641 GLN X 832 GLN Y 134 GLN ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 218 ASN 0 306 HIS 1 130 GLN ** 1 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 129 GLN 2 167 GLN 2 183 ASN Total number of N/Q/H flips: 98 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 63572 Z= 0.203 Angle : 0.682 13.540 86106 Z= 0.351 Chirality : 0.043 0.235 9878 Planarity : 0.006 0.086 10995 Dihedral : 6.067 80.365 8475 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 2.47 % Allowed : 13.43 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.09), residues: 7758 helix: 0.69 (0.08), residues: 4251 sheet: -1.09 (0.17), residues: 826 loop : -2.33 (0.11), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 4 105 HIS 0.009 0.001 HIS N 201 PHE 0.025 0.002 PHE F 172 TYR 0.029 0.002 TYR A 210 ARG 0.016 0.001 ARG W 753 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 883 time to evaluate : 5.477 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: A 77 MET cc_start: 0.1762 (mmp) cc_final: 0.1494 (ptp) REVERT: A 361 MET cc_start: 0.7385 (mmm) cc_final: 0.7067 (mtm) REVERT: A 477 CYS cc_start: 0.2875 (m) cc_final: 0.1837 (m) REVERT: D 92 GLU cc_start: 0.3959 (tm-30) cc_final: 0.3549 (mt-10) REVERT: D 182 MET cc_start: 0.1928 (OUTLIER) cc_final: 0.1543 (mmp) REVERT: G 15 MET cc_start: 0.0253 (mmm) cc_final: -0.2189 (pmm) REVERT: G 44 MET cc_start: 0.1375 (ttp) cc_final: -0.0255 (mmp) REVERT: G 70 MET cc_start: 0.3947 (mmm) cc_final: 0.3736 (mtt) REVERT: G 114 LEU cc_start: 0.5497 (OUTLIER) cc_final: 0.4911 (mt) REVERT: I 76 MET cc_start: 0.3502 (tmm) cc_final: 0.3252 (mpp) REVERT: I 104 MET cc_start: 0.3121 (mmp) cc_final: 0.2329 (tpt) REVERT: K 20 GLU cc_start: 0.1589 (OUTLIER) cc_final: 0.1356 (pt0) REVERT: K 92 MET cc_start: 0.7748 (mmt) cc_final: 0.7267 (mmt) REVERT: N 117 MET cc_start: 0.0074 (tmm) cc_final: -0.0217 (ptm) REVERT: N 227 GLU cc_start: 0.6692 (mp0) cc_final: 0.6479 (mp0) REVERT: N 305 LEU cc_start: 0.8284 (mt) cc_final: 0.7853 (tt) REVERT: N 450 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7215 (mt-10) REVERT: N 458 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7807 (pp) REVERT: N 674 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7038 (tm-30) REVERT: N 703 ARG cc_start: 0.7960 (ptp90) cc_final: 0.7719 (ttp-110) REVERT: N 795 ASN cc_start: 0.7793 (t0) cc_final: 0.7465 (t0) REVERT: N 799 GLU cc_start: 0.4745 (mm-30) cc_final: 0.4506 (mm-30) REVERT: N 870 GLN cc_start: 0.8146 (tp40) cc_final: 0.7559 (tt0) REVERT: O 681 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7608 (mt-10) REVERT: P 30 CYS cc_start: 0.8662 (t) cc_final: 0.8376 (m) REVERT: P 90 ASP cc_start: 0.7528 (t0) cc_final: 0.7290 (t0) REVERT: P 163 LYS cc_start: 0.8410 (tptt) cc_final: 0.8011 (tptt) REVERT: P 232 ASP cc_start: 0.8258 (p0) cc_final: 0.8013 (p0) REVERT: P 382 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8507 (mt) REVERT: P 472 ARG cc_start: 0.8064 (ttm170) cc_final: 0.7830 (mtp180) REVERT: P 598 ASN cc_start: 0.7968 (m-40) cc_final: 0.7564 (t0) REVERT: P 745 LYS cc_start: 0.8343 (mtmm) cc_final: 0.8069 (tppt) REVERT: P 754 ARG cc_start: 0.8287 (tpp-160) cc_final: 0.7912 (tpt170) REVERT: Q 264 GLN cc_start: 0.5819 (tm-30) cc_final: 0.5498 (mp10) REVERT: Q 392 MET cc_start: 0.6274 (tpp) cc_final: 0.6039 (tpp) REVERT: Q 643 MET cc_start: 0.9093 (mtt) cc_final: 0.8888 (mtt) REVERT: R 119 MET cc_start: 0.7684 (mmm) cc_final: 0.7109 (ptt) REVERT: R 121 MET cc_start: 0.4865 (mmm) cc_final: 0.4590 (mtt) REVERT: R 191 GLU cc_start: 0.7318 (pt0) cc_final: 0.6657 (mt-10) REVERT: R 201 LYS cc_start: 0.5933 (ttpt) cc_final: 0.4865 (pptt) REVERT: T 1 MET cc_start: 0.6604 (ptp) cc_final: 0.6062 (ptp) REVERT: T 71 TYR cc_start: 0.7768 (m-80) cc_final: 0.7559 (m-80) REVERT: T 81 ASN cc_start: 0.7675 (t0) cc_final: 0.7244 (t0) REVERT: T 152 ASP cc_start: 0.6889 (m-30) cc_final: 0.6110 (t0) REVERT: T 165 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7672 (mp) REVERT: U 61 LEU cc_start: 0.2359 (tp) cc_final: 0.1115 (pp) REVERT: V 78 LEU cc_start: 0.5402 (tt) cc_final: 0.5041 (mm) REVERT: V 98 ILE cc_start: 0.6075 (mt) cc_final: 0.5749 (mm) REVERT: V 106 ARG cc_start: 0.7867 (ttm110) cc_final: 0.7088 (ttm170) REVERT: V 126 ASP cc_start: 0.7903 (m-30) cc_final: 0.7594 (m-30) REVERT: W 20 GLU cc_start: 0.6951 (mp0) cc_final: 0.6743 (mp0) REVERT: W 27 MET cc_start: 0.7341 (ttm) cc_final: 0.7110 (ttt) REVERT: W 37 LEU cc_start: 0.8361 (mt) cc_final: 0.8154 (mt) REVERT: W 230 VAL cc_start: 0.9566 (t) cc_final: 0.9290 (m) REVERT: W 293 HIS cc_start: 0.6476 (OUTLIER) cc_final: 0.6223 (t-170) REVERT: W 310 TYR cc_start: 0.8491 (t80) cc_final: 0.8279 (t80) REVERT: W 373 MET cc_start: 0.8650 (mmm) cc_final: 0.8320 (mmm) REVERT: W 396 MET cc_start: 0.8688 (mtt) cc_final: 0.8483 (mtp) REVERT: W 716 LEU cc_start: 0.8570 (mt) cc_final: 0.8330 (mt) REVERT: W 770 MET cc_start: 0.3224 (ttt) cc_final: 0.2889 (ptm) REVERT: W 782 MET cc_start: 0.4945 (ptt) cc_final: 0.4621 (ptp) REVERT: W 976 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7523 (mt-10) REVERT: W 1011 TYR cc_start: 0.8557 (t80) cc_final: 0.8254 (t80) REVERT: W 1012 TYR cc_start: 0.8756 (m-80) cc_final: 0.8498 (m-80) REVERT: W 1277 MET cc_start: 0.8778 (mtt) cc_final: 0.8237 (mtp) REVERT: X 29 LYS cc_start: 0.8331 (mttt) cc_final: 0.7869 (tttt) REVERT: X 223 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7527 (mmm160) REVERT: X 265 GLU cc_start: 0.7576 (pt0) cc_final: 0.7346 (pp20) REVERT: X 269 MET cc_start: 0.7940 (tpp) cc_final: 0.7649 (tpp) REVERT: X 301 GLU cc_start: 0.7704 (mp0) cc_final: 0.7364 (mp0) REVERT: X 366 GLU cc_start: 0.7316 (tp30) cc_final: 0.7085 (mm-30) REVERT: X 382 MET cc_start: 0.8556 (mtp) cc_final: 0.8305 (mtp) REVERT: X 630 MET cc_start: 0.8520 (mmm) cc_final: 0.8134 (mmm) REVERT: X 641 GLN cc_start: 0.7819 (mp10) cc_final: 0.7283 (mp10) REVERT: X 642 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8064 (mtm) REVERT: X 654 ASN cc_start: 0.7004 (m-40) cc_final: 0.6694 (t0) REVERT: X 835 ARG cc_start: 0.7198 (ttp-110) cc_final: 0.6986 (tmm-80) REVERT: X 837 ARG cc_start: 0.6800 (mtt180) cc_final: 0.6582 (ttm-80) REVERT: Y 109 GLU cc_start: 0.6456 (pm20) cc_final: 0.6102 (pm20) REVERT: Y 213 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8292 (t) REVERT: Z 482 ARG cc_start: 0.1184 (OUTLIER) cc_final: -0.0019 (tpp80) REVERT: 1 86 ASP cc_start: 0.8669 (t0) cc_final: 0.8346 (m-30) REVERT: 1 103 SER cc_start: 0.9025 (t) cc_final: 0.8719 (m) REVERT: 2 80 GLN cc_start: 0.8241 (mt0) cc_final: 0.7998 (mt0) REVERT: 3 173 MET cc_start: 0.9165 (mtm) cc_final: 0.8914 (mtm) REVERT: 4 75 MET cc_start: 0.0643 (mmm) cc_final: -0.0402 (mtm) REVERT: 4 80 GLN cc_start: 0.2008 (OUTLIER) cc_final: 0.1569 (tp40) REVERT: 4 113 MET cc_start: 0.2276 (mmm) cc_final: 0.0744 (ptm) outliers start: 169 outliers final: 66 residues processed: 1006 average time/residue: 0.5715 time to fit residues: 985.0631 Evaluate side-chains 754 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 677 time to evaluate : 5.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain G residue 72 PHE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 20 GLU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 292 MET Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 820 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 858 MET Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain O residue 735 LEU Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 382 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain P residue 563 LEU Chi-restraints excluded: chain P residue 648 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain T residue 147 CYS Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain W residue 85 MET Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 293 HIS Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 585 ILE Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 908 SER Chi-restraints excluded: chain W residue 970 VAL Chi-restraints excluded: chain W residue 1262 GLU Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 642 MET Chi-restraints excluded: chain X residue 943 VAL Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 213 VAL Chi-restraints excluded: chain Z residue 482 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 177 SER Chi-restraints excluded: chain 0 residue 207 LEU Chi-restraints excluded: chain 1 residue 78 ASP Chi-restraints excluded: chain 1 residue 146 ILE Chi-restraints excluded: chain 2 residue 129 GLN Chi-restraints excluded: chain 4 residue 80 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 394 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 590 optimal weight: 2.9990 chunk 482 optimal weight: 0.2980 chunk 195 optimal weight: 2.9990 chunk 710 optimal weight: 0.9990 chunk 767 optimal weight: 0.9980 chunk 632 optimal weight: 2.9990 chunk 704 optimal weight: 0.7980 chunk 242 optimal weight: 4.9990 chunk 569 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 HIS ** K 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 698 GLN N 804 ASN N 825 ASN N 849 ASN N 964 ASN O 697 HIS P 225 ASN ** P 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 598 ASN P 751 GLN Q 193 HIS Q 219 HIS ** Q 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 626 GLN R 179 GLN T 36 GLN T 162 GLN T 180 HIS ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 4 GLN ** W 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 925 HIS W1198 GLN W1250 HIS X 12 GLN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 483 ASN Z 556 GLN 1 132 HIS 2 183 ASN 3 59 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 63572 Z= 0.293 Angle : 0.672 12.117 86106 Z= 0.344 Chirality : 0.044 0.237 9878 Planarity : 0.005 0.082 10995 Dihedral : 5.502 84.687 8449 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.26 % Favored : 94.60 % Rotamer: Outliers : 3.28 % Allowed : 15.28 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.26 % 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: -0.09 (0.09), residues: 7758 helix: 1.35 (0.08), residues: 4253 sheet: -0.87 (0.17), residues: 834 loop : -2.15 (0.11), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP 4 105 HIS 0.022 0.001 HIS W 293 PHE 0.020 0.002 PHE V 33 TYR 0.021 0.002 TYR W 832 ARG 0.006 0.001 ARG 1 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 723 time to evaluate : 5.363 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: A 77 MET cc_start: 0.1843 (mmp) cc_final: 0.1319 (ptt) REVERT: A 107 MET cc_start: 0.3812 (tpp) cc_final: 0.3446 (tpp) REVERT: A 231 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.5111 (tp) REVERT: A 361 MET cc_start: 0.7524 (mmm) cc_final: 0.7156 (mtm) REVERT: D 72 ARG cc_start: 0.4945 (mmm-85) cc_final: 0.4608 (tpp-160) REVERT: D 182 MET cc_start: 0.2277 (OUTLIER) cc_final: 0.1744 (mmp) REVERT: G 44 MET cc_start: 0.1277 (ttp) cc_final: -0.0273 (mmp) REVERT: G 114 LEU cc_start: 0.5598 (OUTLIER) cc_final: 0.4989 (mt) REVERT: G 162 GLU cc_start: 0.3486 (pp20) cc_final: 0.2684 (tp30) REVERT: H 158 GLU cc_start: 0.2419 (pp20) cc_final: 0.1257 (mm-30) REVERT: I 97 MET cc_start: 0.2727 (ttp) cc_final: 0.2470 (ptm) REVERT: I 104 MET cc_start: 0.3367 (mmp) cc_final: 0.2513 (tpt) REVERT: K 57 GLN cc_start: 0.5507 (tp40) cc_final: 0.4847 (tt0) REVERT: K 92 MET cc_start: 0.7759 (mmt) cc_final: 0.7220 (mmt) REVERT: N 117 MET cc_start: -0.0416 (tmm) cc_final: -0.0675 (ptm) REVERT: N 227 GLU cc_start: 0.6869 (mp0) cc_final: 0.6646 (mp0) REVERT: N 305 LEU cc_start: 0.8345 (mt) cc_final: 0.7957 (tt) REVERT: N 458 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8174 (pp) REVERT: N 674 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7415 (tm-30) REVERT: N 703 ARG cc_start: 0.7964 (ptp90) cc_final: 0.7607 (ttp-110) REVERT: N 795 ASN cc_start: 0.7886 (t0) cc_final: 0.7661 (t0) REVERT: N 849 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8211 (t0) REVERT: N 870 GLN cc_start: 0.8466 (tp40) cc_final: 0.7791 (tt0) REVERT: O 681 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7743 (mt-10) REVERT: O 714 ASP cc_start: 0.7901 (m-30) cc_final: 0.7384 (t0) REVERT: O 766 LYS cc_start: 0.8549 (mttt) cc_final: 0.8273 (mmtp) REVERT: P 30 CYS cc_start: 0.8554 (t) cc_final: 0.8274 (m) REVERT: P 51 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7741 (mp) REVERT: P 382 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8535 (mt) REVERT: P 479 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7720 (mt-10) REVERT: P 598 ASN cc_start: 0.8212 (m110) cc_final: 0.7567 (t0) REVERT: P 745 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8061 (tppt) REVERT: P 754 ARG cc_start: 0.8289 (tpp-160) cc_final: 0.7904 (tpt170) REVERT: Q 264 GLN cc_start: 0.5984 (tm-30) cc_final: 0.5515 (mp10) REVERT: Q 392 MET cc_start: 0.6418 (tpp) cc_final: 0.6047 (tpp) REVERT: R 76 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7197 (mtm) REVERT: R 119 MET cc_start: 0.7693 (mmm) cc_final: 0.7154 (ptt) REVERT: R 191 GLU cc_start: 0.7558 (pt0) cc_final: 0.7056 (mm-30) REVERT: R 201 LYS cc_start: 0.6049 (ttpt) cc_final: 0.4838 (pptt) REVERT: T 1 MET cc_start: 0.6669 (ptp) cc_final: 0.6168 (ptp) REVERT: T 71 TYR cc_start: 0.7865 (m-80) cc_final: 0.7479 (m-80) REVERT: T 81 ASN cc_start: 0.7978 (t0) cc_final: 0.7450 (t0) REVERT: T 153 CYS cc_start: 0.8019 (p) cc_final: 0.7609 (p) REVERT: T 204 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.6192 (pp30) REVERT: U 61 LEU cc_start: 0.2463 (tp) cc_final: 0.1121 (pp) REVERT: V 30 MET cc_start: 0.4883 (mmp) cc_final: 0.3650 (tmm) REVERT: V 78 LEU cc_start: 0.5200 (tt) cc_final: 0.4907 (mm) REVERT: W 20 GLU cc_start: 0.7188 (mp0) cc_final: 0.6953 (mp0) REVERT: W 37 LEU cc_start: 0.8394 (mt) cc_final: 0.8131 (mt) REVERT: W 310 TYR cc_start: 0.8526 (t80) cc_final: 0.8319 (t80) REVERT: W 373 MET cc_start: 0.8657 (mmm) cc_final: 0.8277 (mmm) REVERT: W 393 LEU cc_start: 0.8836 (tp) cc_final: 0.8559 (tp) REVERT: W 396 MET cc_start: 0.8781 (mtt) cc_final: 0.8365 (mtp) REVERT: W 429 TRP cc_start: 0.7501 (m100) cc_final: 0.7291 (m100) REVERT: W 495 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6664 (pt) REVERT: W 782 MET cc_start: 0.5082 (ptt) cc_final: 0.4749 (ptp) REVERT: W 789 PHE cc_start: 0.5927 (t80) cc_final: 0.5623 (t80) REVERT: W 792 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7626 (mt) REVERT: W 796 MET cc_start: 0.7593 (mtt) cc_final: 0.7307 (ttt) REVERT: W 1014 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7672 (tmm) REVERT: W 1277 MET cc_start: 0.8795 (mtt) cc_final: 0.8437 (mtp) REVERT: X 29 LYS cc_start: 0.8534 (mttt) cc_final: 0.7922 (tttt) REVERT: X 223 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7549 (mmm160) REVERT: X 269 MET cc_start: 0.8058 (tpp) cc_final: 0.7676 (tpp) REVERT: X 499 MET cc_start: 0.7691 (mtp) cc_final: 0.7340 (mtp) REVERT: X 654 ASN cc_start: 0.7083 (m-40) cc_final: 0.6771 (t0) REVERT: Y 227 VAL cc_start: 0.8940 (t) cc_final: 0.8568 (m) REVERT: Z 482 ARG cc_start: 0.0965 (OUTLIER) cc_final: -0.0405 (tpp80) REVERT: 0 69 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7161 (tm-30) REVERT: 0 237 GLN cc_start: 0.8253 (mp10) cc_final: 0.7819 (mt0) REVERT: 1 49 GLU cc_start: 0.8190 (tt0) cc_final: 0.7849 (tt0) REVERT: 1 86 ASP cc_start: 0.8704 (t0) cc_final: 0.8363 (m-30) REVERT: 1 103 SER cc_start: 0.9068 (t) cc_final: 0.8794 (m) REVERT: 2 80 GLN cc_start: 0.8261 (mt0) cc_final: 0.8004 (mt0) REVERT: 2 89 ASP cc_start: 0.8330 (m-30) cc_final: 0.7980 (m-30) REVERT: 2 183 ASN cc_start: 0.7801 (m-40) cc_final: 0.6892 (t0) REVERT: 2 186 THR cc_start: 0.5042 (OUTLIER) cc_final: 0.4541 (p) REVERT: 3 173 MET cc_start: 0.9179 (mtm) cc_final: 0.8946 (mtm) REVERT: 4 23 GLU cc_start: 0.3181 (mm-30) cc_final: 0.2841 (mm-30) REVERT: 4 75 MET cc_start: 0.0934 (mmm) cc_final: -0.0153 (mtt) REVERT: 4 80 GLN cc_start: 0.2975 (OUTLIER) cc_final: 0.2031 (tp40) REVERT: 4 105 TRP cc_start: 0.1273 (t60) cc_final: 0.1044 (t60) outliers start: 225 outliers final: 112 residues processed: 896 average time/residue: 0.5649 time to fit residues: 872.4350 Evaluate side-chains 749 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 622 time to evaluate : 5.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 691 LYS Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 820 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 849 ASN Chi-restraints excluded: chain N residue 858 MET Chi-restraints excluded: chain N residue 933 VAL Chi-restraints excluded: chain N residue 950 VAL Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain O residue 735 LEU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 382 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain P residue 457 LEU Chi-restraints excluded: chain P residue 563 LEU Chi-restraints excluded: chain P residue 583 ILE Chi-restraints excluded: chain P residue 608 MET Chi-restraints excluded: chain P residue 714 VAL Chi-restraints excluded: chain P residue 790 CYS Chi-restraints excluded: chain P residue 794 GLU Chi-restraints excluded: chain P residue 803 CYS Chi-restraints excluded: chain P residue 828 LEU Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 159 ILE Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 293 HIS Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 600 ILE Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 792 LEU Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1262 GLU Chi-restraints excluded: chain W residue 1285 SER Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 819 SER Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 224 ARG Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 482 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 177 SER Chi-restraints excluded: chain 0 residue 207 LEU Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 701 optimal weight: 2.9990 chunk 534 optimal weight: 3.9990 chunk 368 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 339 optimal weight: 7.9990 chunk 477 optimal weight: 0.8980 chunk 713 optimal weight: 0.9990 chunk 754 optimal weight: 0.9990 chunk 372 optimal weight: 0.1980 chunk 675 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 374 HIS N 424 ASN ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 697 HIS O 750 GLN ** P 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 517 GLN Q 611 GLN ** T 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 GLN ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 4 GLN W 293 HIS ** W 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1198 GLN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 129 GLN 3 162 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 63572 Z= 0.216 Angle : 0.610 11.131 86106 Z= 0.310 Chirality : 0.042 0.195 9878 Planarity : 0.004 0.072 10995 Dihedral : 5.140 86.032 8441 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.96 % Favored : 94.91 % Rotamer: Outliers : 3.11 % Allowed : 16.46 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.26 % 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: 0.36 (0.10), residues: 7758 helix: 1.73 (0.08), residues: 4262 sheet: -0.67 (0.17), residues: 825 loop : -2.00 (0.11), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 4 105 HIS 0.009 0.001 HIS K 58 PHE 0.022 0.001 PHE V 33 TYR 0.023 0.001 TYR W 832 ARG 0.010 0.000 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 716 time to evaluate : 5.445 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: A 65 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.4550 (pp) REVERT: A 77 MET cc_start: 0.1635 (mmp) cc_final: 0.1080 (ptt) REVERT: A 107 MET cc_start: 0.3802 (tpp) cc_final: 0.3430 (tpp) REVERT: A 270 ILE cc_start: 0.0540 (OUTLIER) cc_final: 0.0139 (mt) REVERT: A 361 MET cc_start: 0.7560 (mmm) cc_final: 0.7022 (mtm) REVERT: A 467 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.6032 (mmt) REVERT: A 477 CYS cc_start: 0.3148 (m) cc_final: 0.2143 (m) REVERT: D 72 ARG cc_start: 0.4843 (mmm-85) cc_final: 0.4605 (tpp-160) REVERT: D 182 MET cc_start: 0.2051 (OUTLIER) cc_final: 0.1698 (mmp) REVERT: F 174 ARG cc_start: 0.5359 (mmt180) cc_final: 0.4468 (ptt-90) REVERT: G 43 MET cc_start: -0.0783 (tmm) cc_final: -0.2630 (pmm) REVERT: G 44 MET cc_start: 0.0934 (ttp) cc_final: -0.0120 (mmt) REVERT: G 114 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.4986 (mt) REVERT: H 158 GLU cc_start: 0.2172 (pp20) cc_final: 0.1017 (mm-30) REVERT: I 104 MET cc_start: 0.2647 (mmp) cc_final: 0.2138 (tpt) REVERT: J 121 MET cc_start: -0.2469 (tpt) cc_final: -0.4257 (ptm) REVERT: K 57 GLN cc_start: 0.5461 (tp40) cc_final: 0.4814 (tt0) REVERT: K 92 MET cc_start: 0.7730 (mmt) cc_final: 0.7297 (mmt) REVERT: N 117 MET cc_start: -0.0210 (tmm) cc_final: -0.0468 (ptm) REVERT: N 227 GLU cc_start: 0.7065 (mp0) cc_final: 0.6505 (mp0) REVERT: N 305 LEU cc_start: 0.8375 (mt) cc_final: 0.7983 (tt) REVERT: N 458 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7936 (pp) REVERT: N 674 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7354 (tm-30) REVERT: N 703 ARG cc_start: 0.7942 (ptp90) cc_final: 0.7609 (ttp-110) REVERT: N 795 ASN cc_start: 0.7878 (t0) cc_final: 0.7676 (t0) REVERT: N 870 GLN cc_start: 0.8396 (tp40) cc_final: 0.7687 (tt0) REVERT: O 681 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7693 (mt-10) REVERT: O 714 ASP cc_start: 0.7906 (m-30) cc_final: 0.7413 (t0) REVERT: O 746 ASN cc_start: 0.7492 (OUTLIER) cc_final: 0.7164 (m-40) REVERT: O 766 LYS cc_start: 0.8545 (mttt) cc_final: 0.8277 (mmtp) REVERT: P 90 ASP cc_start: 0.8024 (t0) cc_final: 0.7817 (t0) REVERT: P 100 ASP cc_start: 0.8681 (p0) cc_final: 0.8404 (p0) REVERT: P 382 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8513 (mt) REVERT: P 598 ASN cc_start: 0.8342 (m110) cc_final: 0.7450 (t0) REVERT: P 745 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8032 (tppt) REVERT: Q 264 GLN cc_start: 0.5987 (tm-30) cc_final: 0.5521 (mp10) REVERT: Q 478 LEU cc_start: 0.8481 (mp) cc_final: 0.8053 (tt) REVERT: R 119 MET cc_start: 0.7661 (mmm) cc_final: 0.7137 (ptt) REVERT: R 191 GLU cc_start: 0.7467 (pt0) cc_final: 0.6540 (mt-10) REVERT: R 201 LYS cc_start: 0.5949 (ttpt) cc_final: 0.4758 (pptt) REVERT: T 1 MET cc_start: 0.6532 (ptp) cc_final: 0.5962 (ptp) REVERT: T 71 TYR cc_start: 0.7813 (m-80) cc_final: 0.7337 (m-80) REVERT: T 81 ASN cc_start: 0.8011 (t0) cc_final: 0.7460 (t0) REVERT: T 153 CYS cc_start: 0.7942 (p) cc_final: 0.7571 (p) REVERT: T 204 GLN cc_start: 0.6546 (OUTLIER) cc_final: 0.6065 (pp30) REVERT: U 61 LEU cc_start: 0.2247 (tp) cc_final: 0.0978 (pp) REVERT: V 30 MET cc_start: 0.5076 (mmp) cc_final: 0.3590 (tmm) REVERT: V 78 LEU cc_start: 0.5124 (tt) cc_final: 0.4829 (mm) REVERT: V 126 ASP cc_start: 0.8219 (m-30) cc_final: 0.7963 (t0) REVERT: W 20 GLU cc_start: 0.7068 (mp0) cc_final: 0.6811 (mp0) REVERT: W 37 LEU cc_start: 0.8446 (mt) cc_final: 0.8178 (mt) REVERT: W 230 VAL cc_start: 0.9535 (t) cc_final: 0.9274 (m) REVERT: W 310 TYR cc_start: 0.8495 (t80) cc_final: 0.8290 (t80) REVERT: W 343 LEU cc_start: 0.8585 (tt) cc_final: 0.8230 (mp) REVERT: W 373 MET cc_start: 0.8690 (mmm) cc_final: 0.8311 (mmm) REVERT: W 393 LEU cc_start: 0.8827 (tp) cc_final: 0.8593 (tp) REVERT: W 396 MET cc_start: 0.8808 (mtt) cc_final: 0.8394 (mtp) REVERT: W 434 ARG cc_start: 0.7736 (ttt-90) cc_final: 0.7335 (ttt-90) REVERT: W 495 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6575 (pt) REVERT: W 770 MET cc_start: 0.2653 (ttt) cc_final: 0.2361 (ptm) REVERT: W 785 SER cc_start: 0.6425 (p) cc_final: 0.6206 (t) REVERT: W 792 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7483 (mt) REVERT: W 796 MET cc_start: 0.7536 (mtt) cc_final: 0.7250 (ttt) REVERT: W 976 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7567 (mt-10) REVERT: W 1012 TYR cc_start: 0.8717 (m-80) cc_final: 0.8430 (m-80) REVERT: W 1014 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7655 (tmm) REVERT: W 1265 ARG cc_start: 0.7601 (mtp85) cc_final: 0.7309 (mtm110) REVERT: W 1277 MET cc_start: 0.8767 (mtt) cc_final: 0.8450 (mtp) REVERT: X 223 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7595 (mmm160) REVERT: X 499 MET cc_start: 0.7653 (mtp) cc_final: 0.7275 (mtp) REVERT: X 654 ASN cc_start: 0.6904 (m-40) cc_final: 0.6623 (t0) REVERT: X 676 ASP cc_start: 0.7851 (p0) cc_final: 0.7639 (p0) REVERT: X 840 ILE cc_start: 0.7821 (pt) cc_final: 0.7609 (pp) REVERT: X 897 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7839 (tt) REVERT: Y 227 VAL cc_start: 0.9006 (t) cc_final: 0.8660 (m) REVERT: Z 482 ARG cc_start: 0.0779 (OUTLIER) cc_final: -0.0577 (tpp80) REVERT: 0 69 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7411 (tm-30) REVERT: 0 237 GLN cc_start: 0.8212 (mp10) cc_final: 0.7958 (mp10) REVERT: 1 49 GLU cc_start: 0.8100 (tt0) cc_final: 0.7858 (tt0) REVERT: 1 86 ASP cc_start: 0.8732 (t0) cc_final: 0.8369 (m-30) REVERT: 1 103 SER cc_start: 0.9053 (t) cc_final: 0.8792 (m) REVERT: 2 80 GLN cc_start: 0.8291 (mt0) cc_final: 0.8038 (mt0) REVERT: 2 183 ASN cc_start: 0.7856 (m-40) cc_final: 0.6812 (t0) REVERT: 2 186 THR cc_start: 0.5081 (OUTLIER) cc_final: 0.4528 (p) REVERT: 3 173 MET cc_start: 0.9184 (mtm) cc_final: 0.8976 (mtm) REVERT: 4 75 MET cc_start: 0.0555 (mmm) cc_final: -0.0061 (mtp) REVERT: 4 80 GLN cc_start: 0.3055 (OUTLIER) cc_final: 0.2064 (tp40) outliers start: 213 outliers final: 116 residues processed: 885 average time/residue: 0.5649 time to fit residues: 859.9720 Evaluate side-chains 775 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 643 time to evaluate : 5.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 424 ASN Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 691 LYS Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 820 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 382 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 563 LEU Chi-restraints excluded: chain P residue 608 MET Chi-restraints excluded: chain P residue 730 ASP Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 790 CYS Chi-restraints excluded: chain P residue 828 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 517 GLN Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 85 MET Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 710 THR Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 792 LEU Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 274 GLN Chi-restraints excluded: chain X residue 529 MET Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 897 LEU Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 224 ARG Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 482 ARG Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 177 SER Chi-restraints excluded: chain 0 residue 207 LEU Chi-restraints excluded: chain 1 residue 146 ILE Chi-restraints excluded: chain 2 residue 133 SER Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 628 optimal weight: 0.8980 chunk 428 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 562 optimal weight: 0.7980 chunk 311 optimal weight: 2.9990 chunk 644 optimal weight: 0.0570 chunk 521 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 385 optimal weight: 0.0030 chunk 677 optimal weight: 0.5980 chunk 190 optimal weight: 0.0030 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 424 ASN ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 732 ASN ** N1179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 697 HIS ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 ASN ** P 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 HIS Q 310 GLN Q 517 GLN R 30 HIS R 192 GLN T 36 GLN T 118 GLN ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 4 GLN ** W 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1198 GLN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 129 GLN ** 4 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 63572 Z= 0.159 Angle : 0.581 10.993 86106 Z= 0.294 Chirality : 0.040 0.215 9878 Planarity : 0.004 0.067 10995 Dihedral : 4.911 87.255 8439 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.87 % Favored : 95.00 % Rotamer: Outliers : 2.83 % Allowed : 17.18 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.26 % 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 (0.10), residues: 7758 helix: 2.00 (0.08), residues: 4264 sheet: -0.51 (0.17), residues: 828 loop : -1.91 (0.11), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 4 105 HIS 0.007 0.001 HIS K 58 PHE 0.018 0.001 PHE N 273 TYR 0.022 0.001 TYR A 225 ARG 0.007 0.000 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 719 time to evaluate : 5.485 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: A 65 LEU cc_start: 0.4953 (OUTLIER) cc_final: 0.4485 (pp) REVERT: A 77 MET cc_start: 0.1577 (mmp) cc_final: 0.0985 (ptt) REVERT: A 107 MET cc_start: 0.3795 (tpp) cc_final: 0.3448 (tpp) REVERT: A 270 ILE cc_start: 0.0726 (OUTLIER) cc_final: 0.0339 (mt) REVERT: A 361 MET cc_start: 0.7453 (mmm) cc_final: 0.7092 (mtm) REVERT: A 467 MET cc_start: 0.6489 (OUTLIER) cc_final: 0.6123 (mmt) REVERT: A 477 CYS cc_start: 0.3023 (m) cc_final: 0.2050 (m) REVERT: D 66 LEU cc_start: 0.3509 (OUTLIER) cc_final: 0.3102 (mp) REVERT: D 75 GLU cc_start: 0.6092 (pt0) cc_final: 0.5259 (tp30) REVERT: D 88 LYS cc_start: 0.5425 (mttt) cc_final: 0.5005 (mttm) REVERT: D 108 GLN cc_start: 0.5686 (pt0) cc_final: 0.3820 (mm-40) REVERT: D 182 MET cc_start: 0.1821 (OUTLIER) cc_final: 0.1409 (mmp) REVERT: G 43 MET cc_start: -0.0817 (tmm) cc_final: -0.2568 (pmm) REVERT: G 44 MET cc_start: 0.1393 (ttp) cc_final: 0.0133 (mmt) REVERT: G 114 LEU cc_start: 0.5364 (OUTLIER) cc_final: 0.4791 (mt) REVERT: G 138 MET cc_start: 0.1167 (ptt) cc_final: 0.0873 (ptm) REVERT: H 158 GLU cc_start: 0.2198 (pp20) cc_final: 0.0995 (mm-30) REVERT: I 104 MET cc_start: 0.2511 (mmp) cc_final: 0.2130 (tpt) REVERT: J 121 MET cc_start: -0.2534 (tpt) cc_final: -0.4240 (ptt) REVERT: K 57 GLN cc_start: 0.5343 (tp40) cc_final: 0.4799 (tt0) REVERT: K 92 MET cc_start: 0.7657 (mmt) cc_final: 0.7161 (mmt) REVERT: N 117 MET cc_start: -0.0189 (tmm) cc_final: -0.0479 (ptm) REVERT: N 227 GLU cc_start: 0.7044 (mp0) cc_final: 0.6633 (mp0) REVERT: N 305 LEU cc_start: 0.8397 (mt) cc_final: 0.7906 (tt) REVERT: N 547 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: N 674 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7350 (tm-30) REVERT: N 691 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8667 (tptp) REVERT: N 703 ARG cc_start: 0.7953 (ptp90) cc_final: 0.7627 (ttp-110) REVERT: N 870 GLN cc_start: 0.8347 (tp40) cc_final: 0.7670 (tt0) REVERT: O 681 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7614 (mt-10) REVERT: O 714 ASP cc_start: 0.7912 (m-30) cc_final: 0.7404 (t0) REVERT: O 766 LYS cc_start: 0.8485 (mttt) cc_final: 0.8237 (mmtp) REVERT: P 51 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7820 (mp) REVERT: P 100 ASP cc_start: 0.8585 (p0) cc_final: 0.8236 (p0) REVERT: P 102 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8434 (p0) REVERT: P 382 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8479 (mt) REVERT: P 598 ASN cc_start: 0.8272 (m110) cc_final: 0.7607 (t0) REVERT: P 745 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8021 (tppt) REVERT: Q 264 GLN cc_start: 0.5908 (tm-30) cc_final: 0.5537 (mp10) REVERT: Q 478 LEU cc_start: 0.8443 (mp) cc_final: 0.8061 (tt) REVERT: R 119 MET cc_start: 0.7465 (mmm) cc_final: 0.7110 (ptt) REVERT: R 191 GLU cc_start: 0.7340 (pt0) cc_final: 0.6516 (mt-10) REVERT: R 201 LYS cc_start: 0.6030 (ttpt) cc_final: 0.4909 (pptt) REVERT: T 1 MET cc_start: 0.6404 (ptp) cc_final: 0.5875 (ptp) REVERT: T 63 MET cc_start: 0.4670 (ppp) cc_final: 0.3994 (ppp) REVERT: T 71 TYR cc_start: 0.7830 (m-80) cc_final: 0.7367 (m-80) REVERT: T 81 ASN cc_start: 0.7824 (t0) cc_final: 0.7344 (t0) REVERT: T 153 CYS cc_start: 0.7897 (p) cc_final: 0.7485 (p) REVERT: T 204 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6031 (pp30) REVERT: U 61 LEU cc_start: 0.2190 (tp) cc_final: 0.0894 (pp) REVERT: V 78 LEU cc_start: 0.5151 (tt) cc_final: 0.4881 (mm) REVERT: W 4 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: W 20 GLU cc_start: 0.6982 (mp0) cc_final: 0.6710 (mp0) REVERT: W 37 LEU cc_start: 0.8469 (mt) cc_final: 0.8217 (mt) REVERT: W 230 VAL cc_start: 0.9517 (t) cc_final: 0.9257 (m) REVERT: W 310 TYR cc_start: 0.8474 (t80) cc_final: 0.8247 (t80) REVERT: W 343 LEU cc_start: 0.8627 (tt) cc_final: 0.8278 (mp) REVERT: W 373 MET cc_start: 0.8675 (mmm) cc_final: 0.8298 (mmm) REVERT: W 393 LEU cc_start: 0.8815 (tp) cc_final: 0.8604 (tp) REVERT: W 396 MET cc_start: 0.8816 (mtt) cc_final: 0.8401 (mtp) REVERT: W 792 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7627 (mt) REVERT: W 797 LEU cc_start: 0.8573 (mt) cc_final: 0.8259 (mt) REVERT: W 1012 TYR cc_start: 0.8687 (m-80) cc_final: 0.8355 (m-80) REVERT: W 1014 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7632 (tmm) REVERT: W 1277 MET cc_start: 0.8744 (mtt) cc_final: 0.8397 (mtp) REVERT: X 223 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7503 (mmm160) REVERT: X 499 MET cc_start: 0.7638 (mtp) cc_final: 0.7283 (mtp) REVERT: X 654 ASN cc_start: 0.6846 (m-40) cc_final: 0.6431 (t0) REVERT: X 676 ASP cc_start: 0.7776 (p0) cc_final: 0.7569 (p0) REVERT: Y 104 MET cc_start: 0.7869 (ptt) cc_final: 0.7565 (ptt) REVERT: Y 227 VAL cc_start: 0.9003 (t) cc_final: 0.8661 (m) REVERT: 0 69 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7467 (tm-30) REVERT: 0 237 GLN cc_start: 0.8131 (mp10) cc_final: 0.7815 (mp10) REVERT: 1 86 ASP cc_start: 0.8725 (t0) cc_final: 0.8344 (m-30) REVERT: 1 103 SER cc_start: 0.9072 (t) cc_final: 0.8831 (m) REVERT: 1 144 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7298 (tp30) REVERT: 2 80 GLN cc_start: 0.8273 (mt0) cc_final: 0.8024 (mt0) REVERT: 2 89 ASP cc_start: 0.7940 (m-30) cc_final: 0.7639 (m-30) REVERT: 2 129 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: 2 183 ASN cc_start: 0.7758 (m-40) cc_final: 0.6769 (t0) REVERT: 2 186 THR cc_start: 0.5335 (OUTLIER) cc_final: 0.4980 (p) REVERT: 3 173 MET cc_start: 0.9159 (mtm) cc_final: 0.8919 (mtm) REVERT: 4 75 MET cc_start: 0.0621 (mmm) cc_final: 0.0388 (mmm) REVERT: 4 80 GLN cc_start: 0.2806 (OUTLIER) cc_final: 0.1804 (tp40) outliers start: 194 outliers final: 98 residues processed: 864 average time/residue: 0.5618 time to fit residues: 836.1679 Evaluate side-chains 760 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 643 time to evaluate : 5.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 691 LYS Chi-restraints excluded: chain N residue 697 THR Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 802 VAL Chi-restraints excluded: chain N residue 804 ASN Chi-restraints excluded: chain N residue 820 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 382 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 608 MET Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 790 CYS Chi-restraints excluded: chain P residue 828 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 324 HIS Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 85 MET Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 293 HIS Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 710 THR Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 792 LEU Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain W residue 1198 GLN Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 2 residue 129 GLN Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 253 optimal weight: 0.6980 chunk 679 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 443 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 755 optimal weight: 0.8980 chunk 627 optimal weight: 0.8980 chunk 349 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 249 optimal weight: 0.6980 chunk 396 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 HIS ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 424 ASN ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 697 HIS ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 ASN P 494 HIS R 97 ASN R 192 GLN ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 GLN ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 428 HIS ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 129 GLN ** 4 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 63572 Z= 0.209 Angle : 0.593 10.746 86106 Z= 0.299 Chirality : 0.041 0.227 9878 Planarity : 0.004 0.063 10995 Dihedral : 4.764 88.621 8432 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.03 % Favored : 94.86 % Rotamer: Outliers : 2.88 % Allowed : 17.76 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.26 % 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: 0.80 (0.10), residues: 7758 helix: 2.08 (0.08), residues: 4272 sheet: -0.41 (0.18), residues: 834 loop : -1.85 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 4 105 HIS 0.008 0.001 HIS K 58 PHE 0.017 0.001 PHE X 744 TYR 0.022 0.001 TYR 4 51 ARG 0.006 0.000 ARG X 835 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 678 time to evaluate : 6.264 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: A 65 LEU cc_start: 0.4768 (OUTLIER) cc_final: 0.4565 (mm) REVERT: A 77 MET cc_start: 0.1399 (mmp) cc_final: 0.1141 (ptt) REVERT: A 107 MET cc_start: 0.3894 (tpp) cc_final: 0.3572 (tpp) REVERT: A 270 ILE cc_start: 0.0578 (OUTLIER) cc_final: 0.0207 (mt) REVERT: A 361 MET cc_start: 0.7440 (mmm) cc_final: 0.7187 (mtm) REVERT: A 502 MET cc_start: 0.6241 (ttt) cc_final: 0.5979 (ttt) REVERT: D 66 LEU cc_start: 0.3544 (OUTLIER) cc_final: 0.3295 (mp) REVERT: D 108 GLN cc_start: 0.5672 (pt0) cc_final: 0.3852 (mm-40) REVERT: D 180 LEU cc_start: 0.4336 (OUTLIER) cc_final: 0.4108 (pp) REVERT: D 182 MET cc_start: 0.1890 (OUTLIER) cc_final: 0.1458 (mmp) REVERT: G 43 MET cc_start: -0.0803 (OUTLIER) cc_final: -0.2280 (pmm) REVERT: G 44 MET cc_start: 0.1207 (ttp) cc_final: 0.0174 (mmp) REVERT: G 114 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.4808 (mt) REVERT: G 138 MET cc_start: 0.1450 (ptt) cc_final: 0.1176 (ptm) REVERT: H 158 GLU cc_start: 0.2563 (pp20) cc_final: 0.1073 (mm-30) REVERT: I 104 MET cc_start: 0.2727 (mmp) cc_final: 0.2107 (tpt) REVERT: J 121 MET cc_start: -0.2628 (tpt) cc_final: -0.4335 (ptt) REVERT: K 57 GLN cc_start: 0.5275 (tp40) cc_final: 0.4653 (tt0) REVERT: K 77 GLN cc_start: 0.6767 (mm-40) cc_final: 0.6536 (mm-40) REVERT: K 92 MET cc_start: 0.7643 (mmt) cc_final: 0.7164 (mmt) REVERT: N 117 MET cc_start: -0.0152 (tmm) cc_final: -0.0473 (ptm) REVERT: N 227 GLU cc_start: 0.7097 (mp0) cc_final: 0.6687 (mp0) REVERT: N 305 LEU cc_start: 0.8412 (mt) cc_final: 0.7985 (tt) REVERT: N 547 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7299 (pt0) REVERT: N 674 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7354 (tm-30) REVERT: N 691 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8655 (tptp) REVERT: N 703 ARG cc_start: 0.7962 (ptp90) cc_final: 0.7624 (ttp-110) REVERT: N 830 LYS cc_start: 0.7756 (mttt) cc_final: 0.7143 (mtmm) REVERT: O 681 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7692 (mt-10) REVERT: O 714 ASP cc_start: 0.8003 (m-30) cc_final: 0.7505 (t0) REVERT: O 739 ARG cc_start: 0.7689 (mmt90) cc_final: 0.7435 (mmt90) REVERT: O 766 LYS cc_start: 0.8516 (mttt) cc_final: 0.8267 (mmtp) REVERT: P 51 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7824 (mp) REVERT: P 100 ASP cc_start: 0.8636 (p0) cc_final: 0.8326 (p0) REVERT: P 171 PHE cc_start: 0.8384 (t80) cc_final: 0.7963 (t80) REVERT: P 598 ASN cc_start: 0.8363 (m110) cc_final: 0.7748 (t0) REVERT: P 745 LYS cc_start: 0.8335 (mtmm) cc_final: 0.8002 (tppt) REVERT: Q 264 GLN cc_start: 0.5950 (tm-30) cc_final: 0.5559 (mp10) REVERT: Q 478 LEU cc_start: 0.8459 (mp) cc_final: 0.8084 (tt) REVERT: Q 493 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8954 (mp) REVERT: R 76 MET cc_start: 0.7027 (mtm) cc_final: 0.6596 (pmm) REVERT: R 119 MET cc_start: 0.7455 (mmm) cc_final: 0.7093 (ptt) REVERT: R 191 GLU cc_start: 0.7364 (pt0) cc_final: 0.6915 (mm-30) REVERT: R 201 LYS cc_start: 0.5920 (ttpt) cc_final: 0.4833 (pptt) REVERT: T 1 MET cc_start: 0.6404 (ptp) cc_final: 0.5852 (ptp) REVERT: T 63 MET cc_start: 0.4613 (ppp) cc_final: 0.3924 (ppp) REVERT: T 71 TYR cc_start: 0.7877 (m-80) cc_final: 0.7364 (m-80) REVERT: T 81 ASN cc_start: 0.8083 (t0) cc_final: 0.7533 (t0) REVERT: T 153 CYS cc_start: 0.7953 (p) cc_final: 0.7577 (p) REVERT: T 204 GLN cc_start: 0.6675 (OUTLIER) cc_final: 0.6107 (pp30) REVERT: U 61 LEU cc_start: 0.2202 (tp) cc_final: 0.0863 (pp) REVERT: V 24 ASP cc_start: 0.5431 (m-30) cc_final: 0.5087 (m-30) REVERT: V 78 LEU cc_start: 0.5118 (tt) cc_final: 0.4871 (mm) REVERT: V 103 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7425 (tm-30) REVERT: W 4 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: W 20 GLU cc_start: 0.7026 (mp0) cc_final: 0.6772 (mp0) REVERT: W 37 LEU cc_start: 0.8477 (mt) cc_final: 0.8221 (mt) REVERT: W 230 VAL cc_start: 0.9520 (t) cc_final: 0.9250 (m) REVERT: W 310 TYR cc_start: 0.8470 (t80) cc_final: 0.8235 (t80) REVERT: W 343 LEU cc_start: 0.8607 (tt) cc_final: 0.8252 (mp) REVERT: W 373 MET cc_start: 0.8722 (mmm) cc_final: 0.8417 (mmm) REVERT: W 396 MET cc_start: 0.8825 (mtt) cc_final: 0.8423 (mtp) REVERT: W 495 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6752 (pt) REVERT: W 574 MET cc_start: 0.8517 (mmt) cc_final: 0.8290 (mmt) REVERT: W 1012 TYR cc_start: 0.8717 (m-80) cc_final: 0.8427 (m-80) REVERT: W 1014 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7630 (tmm) REVERT: W 1158 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: W 1277 MET cc_start: 0.8765 (mtt) cc_final: 0.8415 (mtp) REVERT: X 223 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7538 (mmm160) REVERT: X 499 MET cc_start: 0.7640 (mtp) cc_final: 0.7257 (mtp) REVERT: X 654 ASN cc_start: 0.6829 (m-40) cc_final: 0.6414 (t0) REVERT: X 676 ASP cc_start: 0.7814 (p0) cc_final: 0.7592 (p0) REVERT: X 893 MET cc_start: 0.8901 (mmm) cc_final: 0.8645 (tpp) REVERT: Y 104 MET cc_start: 0.7990 (ptt) cc_final: 0.7682 (ptp) REVERT: Y 227 VAL cc_start: 0.9018 (t) cc_final: 0.8697 (m) REVERT: 0 69 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7548 (tm-30) REVERT: 0 237 GLN cc_start: 0.8201 (mp10) cc_final: 0.7831 (mp10) REVERT: 0 300 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8011 (ptm160) REVERT: 1 49 GLU cc_start: 0.8105 (tt0) cc_final: 0.7704 (tt0) REVERT: 1 86 ASP cc_start: 0.8692 (t0) cc_final: 0.8269 (m-30) REVERT: 1 103 SER cc_start: 0.9058 (t) cc_final: 0.8802 (m) REVERT: 1 144 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: 2 80 GLN cc_start: 0.8284 (mt0) cc_final: 0.8035 (mt0) REVERT: 2 183 ASN cc_start: 0.7737 (m-40) cc_final: 0.6688 (t0) REVERT: 2 186 THR cc_start: 0.5058 (OUTLIER) cc_final: 0.4810 (p) REVERT: 3 173 MET cc_start: 0.9147 (mtm) cc_final: 0.8945 (mtm) REVERT: 4 23 GLU cc_start: 0.2727 (mm-30) cc_final: 0.2414 (mm-30) REVERT: 4 80 GLN cc_start: 0.3119 (OUTLIER) cc_final: 0.2045 (tp40) outliers start: 197 outliers final: 124 residues processed: 829 average time/residue: 0.5625 time to fit residues: 809.5722 Evaluate side-chains 781 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 637 time to evaluate : 5.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 691 LYS Chi-restraints excluded: chain N residue 697 THR Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 802 VAL Chi-restraints excluded: chain N residue 804 ASN Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 608 MET Chi-restraints excluded: chain P residue 648 ASP Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 790 CYS Chi-restraints excluded: chain P residue 803 CYS Chi-restraints excluded: chain P residue 828 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 245 VAL Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 324 HIS Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 493 LEU Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 570 THR Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1158 GLU Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 180 ILE Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 274 GLN Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 830 THR Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 300 ARG Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 728 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 430 optimal weight: 0.7980 chunk 551 optimal weight: 0.6980 chunk 427 optimal weight: 2.9990 chunk 636 optimal weight: 0.6980 chunk 421 optimal weight: 0.8980 chunk 752 optimal weight: 0.8980 chunk 471 optimal weight: 0.8980 chunk 458 optimal weight: 0.9990 chunk 347 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 424 ASN ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 697 HIS ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 ASN ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 GLN ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 4 GLN W 345 GLN ** W 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 175 HIS ** 4 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 63572 Z= 0.203 Angle : 0.590 10.812 86106 Z= 0.297 Chirality : 0.041 0.308 9878 Planarity : 0.004 0.070 10995 Dihedral : 4.707 89.979 8432 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.13 % Favored : 94.77 % Rotamer: Outliers : 2.92 % Allowed : 18.03 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.26 % 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: 0.94 (0.10), residues: 7758 helix: 2.19 (0.08), residues: 4270 sheet: -0.34 (0.18), residues: 816 loop : -1.77 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 4 105 HIS 0.010 0.001 HIS P 387 PHE 0.016 0.001 PHE X 340 TYR 0.015 0.001 TYR R 167 ARG 0.013 0.000 ARG P 812 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 662 time to evaluate : 5.803 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: A 77 MET cc_start: 0.1546 (mmp) cc_final: 0.1225 (ptt) REVERT: A 107 MET cc_start: 0.3772 (tpp) cc_final: 0.3458 (tpp) REVERT: A 361 MET cc_start: 0.7522 (mmm) cc_final: 0.7160 (mtm) REVERT: D 66 LEU cc_start: 0.3358 (OUTLIER) cc_final: 0.3141 (mp) REVERT: D 108 GLN cc_start: 0.5424 (pt0) cc_final: 0.3662 (mm110) REVERT: D 180 LEU cc_start: 0.4371 (OUTLIER) cc_final: 0.4096 (pp) REVERT: D 182 MET cc_start: 0.2292 (OUTLIER) cc_final: 0.2055 (mmp) REVERT: G 26 ILE cc_start: 0.1466 (tp) cc_final: 0.1194 (tp) REVERT: G 43 MET cc_start: -0.0823 (OUTLIER) cc_final: -0.2487 (pmm) REVERT: G 44 MET cc_start: 0.1661 (ttp) cc_final: 0.0802 (mmt) REVERT: G 114 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.4947 (mt) REVERT: G 138 MET cc_start: 0.1520 (ptt) cc_final: 0.1018 (ptm) REVERT: H 158 GLU cc_start: 0.2581 (pp20) cc_final: 0.1102 (mm-30) REVERT: I 104 MET cc_start: 0.2939 (mmp) cc_final: 0.2277 (tpt) REVERT: J 121 MET cc_start: -0.2630 (tpt) cc_final: -0.4235 (ptt) REVERT: K 92 MET cc_start: 0.7629 (mmt) cc_final: 0.7173 (mmt) REVERT: N 117 MET cc_start: -0.0189 (tmm) cc_final: -0.0526 (ptm) REVERT: N 227 GLU cc_start: 0.7149 (mp0) cc_final: 0.6733 (mp0) REVERT: N 305 LEU cc_start: 0.8435 (mt) cc_final: 0.7897 (tt) REVERT: N 547 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7184 (pt0) REVERT: N 674 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7456 (tm-30) REVERT: N 830 LYS cc_start: 0.7769 (mttt) cc_final: 0.7174 (mtmm) REVERT: O 681 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7733 (mt-10) REVERT: O 714 ASP cc_start: 0.7985 (m-30) cc_final: 0.7444 (t0) REVERT: O 739 ARG cc_start: 0.7728 (mmt90) cc_final: 0.7491 (mmt90) REVERT: O 766 LYS cc_start: 0.8440 (mttt) cc_final: 0.8175 (mmtp) REVERT: P 51 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7871 (mp) REVERT: P 100 ASP cc_start: 0.8642 (p0) cc_final: 0.8336 (p0) REVERT: P 171 PHE cc_start: 0.8366 (t80) cc_final: 0.7793 (t80) REVERT: P 745 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7937 (ttmt) REVERT: Q 264 GLN cc_start: 0.6091 (tm-30) cc_final: 0.5608 (mp10) REVERT: Q 478 LEU cc_start: 0.8414 (mp) cc_final: 0.8083 (tt) REVERT: Q 493 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8946 (mp) REVERT: R 76 MET cc_start: 0.6733 (mtm) cc_final: 0.6464 (pmm) REVERT: R 119 MET cc_start: 0.7458 (mmm) cc_final: 0.7116 (ptt) REVERT: R 191 GLU cc_start: 0.7144 (pt0) cc_final: 0.6822 (mm-30) REVERT: R 201 LYS cc_start: 0.6103 (ttpt) cc_final: 0.4910 (pptt) REVERT: T 1 MET cc_start: 0.6306 (ptp) cc_final: 0.5739 (ptp) REVERT: T 63 MET cc_start: 0.4647 (ppp) cc_final: 0.3935 (ppp) REVERT: T 81 ASN cc_start: 0.8092 (t0) cc_final: 0.7526 (t0) REVERT: T 153 CYS cc_start: 0.7951 (p) cc_final: 0.7611 (p) REVERT: U 61 LEU cc_start: 0.2163 (tp) cc_final: 0.0769 (pp) REVERT: V 78 LEU cc_start: 0.5075 (tt) cc_final: 0.4847 (mm) REVERT: V 126 ASP cc_start: 0.7957 (t0) cc_final: 0.7380 (t0) REVERT: W 20 GLU cc_start: 0.7035 (mp0) cc_final: 0.6738 (mp0) REVERT: W 37 LEU cc_start: 0.8506 (mt) cc_final: 0.8241 (mt) REVERT: W 230 VAL cc_start: 0.9516 (t) cc_final: 0.9247 (m) REVERT: W 310 TYR cc_start: 0.8455 (t80) cc_final: 0.8213 (t80) REVERT: W 343 LEU cc_start: 0.8636 (tt) cc_final: 0.8323 (mp) REVERT: W 373 MET cc_start: 0.8725 (mmm) cc_final: 0.8333 (mmm) REVERT: W 396 MET cc_start: 0.8889 (mtt) cc_final: 0.8436 (mtp) REVERT: W 495 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6753 (pt) REVERT: W 791 CYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8136 (m) REVERT: W 1012 TYR cc_start: 0.8712 (m-80) cc_final: 0.8371 (m-80) REVERT: W 1014 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7606 (tmm) REVERT: W 1158 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: W 1277 MET cc_start: 0.8763 (mtt) cc_final: 0.8413 (mtp) REVERT: X 223 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7541 (mmm160) REVERT: X 499 MET cc_start: 0.7569 (mtp) cc_final: 0.7225 (mtp) REVERT: X 676 ASP cc_start: 0.7819 (p0) cc_final: 0.7599 (p0) REVERT: X 893 MET cc_start: 0.8929 (mmm) cc_final: 0.8547 (tpp) REVERT: Y 104 MET cc_start: 0.7873 (ptt) cc_final: 0.7600 (ptt) REVERT: Y 135 ILE cc_start: 0.7462 (mp) cc_final: 0.6958 (mt) REVERT: Y 227 VAL cc_start: 0.8996 (t) cc_final: 0.8744 (m) REVERT: 0 69 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7581 (tm-30) REVERT: 0 237 GLN cc_start: 0.8214 (mp10) cc_final: 0.7897 (mp10) REVERT: 0 300 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7978 (ptm160) REVERT: 0 301 THR cc_start: 0.7814 (p) cc_final: 0.7308 (p) REVERT: 0 303 GLU cc_start: 0.7770 (mp0) cc_final: 0.7299 (pm20) REVERT: 1 49 GLU cc_start: 0.8161 (tt0) cc_final: 0.7896 (tt0) REVERT: 1 86 ASP cc_start: 0.8652 (t0) cc_final: 0.8252 (m-30) REVERT: 1 103 SER cc_start: 0.9068 (t) cc_final: 0.8822 (m) REVERT: 1 144 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7359 (tp30) REVERT: 2 68 LYS cc_start: 0.8165 (mttp) cc_final: 0.7834 (mmmt) REVERT: 2 89 ASP cc_start: 0.7934 (m-30) cc_final: 0.7647 (m-30) REVERT: 2 183 ASN cc_start: 0.7775 (m-40) cc_final: 0.6686 (t0) REVERT: 2 186 THR cc_start: 0.5082 (OUTLIER) cc_final: 0.4684 (p) REVERT: 3 173 MET cc_start: 0.9165 (mtm) cc_final: 0.8934 (mtm) REVERT: 4 23 GLU cc_start: 0.2999 (mm-30) cc_final: 0.2628 (mm-30) REVERT: 4 80 GLN cc_start: 0.2957 (OUTLIER) cc_final: 0.2014 (tp40) outliers start: 200 outliers final: 134 residues processed: 827 average time/residue: 0.5507 time to fit residues: 796.3735 Evaluate side-chains 769 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 619 time to evaluate : 5.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 424 ASN Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 697 THR Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 802 VAL Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 933 VAL Chi-restraints excluded: chain N residue 950 VAL Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 348 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 556 ILE Chi-restraints excluded: chain P residue 685 SER Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 790 CYS Chi-restraints excluded: chain P residue 794 GLU Chi-restraints excluded: chain P residue 803 CYS Chi-restraints excluded: chain P residue 828 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 493 LEU Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 570 THR Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 674 THR Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 710 THR Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 791 CYS Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1158 GLU Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 180 ILE Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 819 SER Chi-restraints excluded: chain X residue 830 THR Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 0 residue 276 LEU Chi-restraints excluded: chain 0 residue 300 ARG Chi-restraints excluded: chain 1 residue 110 VAL Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 465 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 chunk 449 optimal weight: 5.9990 chunk 226 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 145 optimal weight: 220.0000 chunk 478 optimal weight: 0.9980 chunk 512 optimal weight: 4.9990 chunk 372 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 591 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 77 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 424 ASN ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 697 HIS O 705 HIS ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 ASN T 103 GLN U 28 GLN U 129 GLN ** W 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 266 GLN ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 63572 Z= 0.226 Angle : 0.610 12.828 86106 Z= 0.306 Chirality : 0.041 0.283 9878 Planarity : 0.004 0.060 10995 Dihedral : 4.698 88.832 8432 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Rotamer: Outliers : 2.89 % Allowed : 18.41 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.26 % 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: 0.96 (0.10), residues: 7758 helix: 2.20 (0.08), residues: 4270 sheet: -0.32 (0.18), residues: 808 loop : -1.75 (0.12), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 4 105 HIS 0.008 0.001 HIS K 58 PHE 0.024 0.001 PHE W 608 TYR 0.019 0.001 TYR R 167 ARG 0.007 0.000 ARG P 812 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 645 time to evaluate : 5.366 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: A 107 MET cc_start: 0.3792 (tpp) cc_final: 0.3530 (tpp) REVERT: A 361 MET cc_start: 0.7522 (mmm) cc_final: 0.7094 (mtm) REVERT: D 66 LEU cc_start: 0.3403 (OUTLIER) cc_final: 0.3182 (mp) REVERT: D 88 LYS cc_start: 0.5506 (mttt) cc_final: 0.5096 (mttm) REVERT: D 108 GLN cc_start: 0.5381 (pt0) cc_final: 0.3627 (mm110) REVERT: D 180 LEU cc_start: 0.4346 (OUTLIER) cc_final: 0.4046 (pp) REVERT: G 26 ILE cc_start: 0.1732 (tp) cc_final: 0.1505 (tp) REVERT: G 43 MET cc_start: -0.1424 (OUTLIER) cc_final: -0.2072 (pmm) REVERT: G 44 MET cc_start: 0.1588 (ttp) cc_final: 0.0741 (mmp) REVERT: G 114 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.4963 (mt) REVERT: H 158 GLU cc_start: 0.2605 (pp20) cc_final: 0.1068 (mm-30) REVERT: I 104 MET cc_start: 0.2937 (mmp) cc_final: 0.2033 (tpt) REVERT: J 121 MET cc_start: -0.2581 (tpt) cc_final: -0.4282 (ptt) REVERT: K 77 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6577 (mm110) REVERT: K 92 MET cc_start: 0.7584 (mmt) cc_final: 0.7153 (mmt) REVERT: N 117 MET cc_start: -0.0167 (tmm) cc_final: -0.0576 (ptm) REVERT: N 227 GLU cc_start: 0.7266 (mp0) cc_final: 0.6832 (mp0) REVERT: N 305 LEU cc_start: 0.8418 (mt) cc_final: 0.7954 (tt) REVERT: N 547 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7403 (pt0) REVERT: N 674 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7496 (tm-30) REVERT: N 830 LYS cc_start: 0.7792 (mttt) cc_final: 0.7212 (mtmm) REVERT: O 681 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7781 (mt-10) REVERT: O 714 ASP cc_start: 0.8050 (m-30) cc_final: 0.7462 (t0) REVERT: O 739 ARG cc_start: 0.7771 (mmt90) cc_final: 0.7534 (mmt90) REVERT: O 766 LYS cc_start: 0.8467 (mttt) cc_final: 0.8219 (mmtp) REVERT: P 100 ASP cc_start: 0.8667 (p0) cc_final: 0.8389 (p0) REVERT: P 745 LYS cc_start: 0.8296 (mtmm) cc_final: 0.7977 (ttmt) REVERT: Q 251 LEU cc_start: 0.8588 (mt) cc_final: 0.8379 (mt) REVERT: Q 264 GLN cc_start: 0.6121 (tm-30) cc_final: 0.5628 (mp10) REVERT: Q 415 LYS cc_start: 0.7966 (mttt) cc_final: 0.7347 (tptp) REVERT: Q 478 LEU cc_start: 0.8422 (mp) cc_final: 0.8084 (tt) REVERT: Q 493 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8945 (mp) REVERT: R 119 MET cc_start: 0.7438 (mmm) cc_final: 0.7200 (ptt) REVERT: R 191 GLU cc_start: 0.7281 (pt0) cc_final: 0.6852 (mm-30) REVERT: R 201 LYS cc_start: 0.6162 (ttpt) cc_final: 0.4939 (pptt) REVERT: T 1 MET cc_start: 0.6311 (ptp) cc_final: 0.5669 (ptp) REVERT: T 81 ASN cc_start: 0.8122 (t0) cc_final: 0.7540 (t0) REVERT: T 153 CYS cc_start: 0.7986 (p) cc_final: 0.7636 (p) REVERT: U 1 MET cc_start: 0.3410 (tpt) cc_final: 0.1630 (mmt) REVERT: U 61 LEU cc_start: 0.1817 (tp) cc_final: 0.0461 (pp) REVERT: V 78 LEU cc_start: 0.5050 (tt) cc_final: 0.4807 (mm) REVERT: W 20 GLU cc_start: 0.6986 (mp0) cc_final: 0.6690 (mp0) REVERT: W 37 LEU cc_start: 0.8499 (mt) cc_final: 0.8242 (mt) REVERT: W 310 TYR cc_start: 0.8427 (t80) cc_final: 0.8218 (t80) REVERT: W 343 LEU cc_start: 0.8655 (tt) cc_final: 0.8352 (mp) REVERT: W 373 MET cc_start: 0.8707 (mmm) cc_final: 0.8316 (mmm) REVERT: W 396 MET cc_start: 0.8900 (mtt) cc_final: 0.8558 (mtp) REVERT: W 495 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6799 (pt) REVERT: W 739 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8452 (mp) REVERT: W 834 PHE cc_start: 0.7222 (m-80) cc_final: 0.6900 (m-80) REVERT: W 1012 TYR cc_start: 0.8715 (m-80) cc_final: 0.8347 (m-80) REVERT: W 1014 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7586 (tmm) REVERT: W 1158 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: W 1277 MET cc_start: 0.8764 (mtt) cc_final: 0.8410 (mtp) REVERT: X 223 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7558 (mmm160) REVERT: X 499 MET cc_start: 0.7564 (mtp) cc_final: 0.7235 (mtp) REVERT: X 676 ASP cc_start: 0.7822 (p0) cc_final: 0.7598 (p0) REVERT: X 893 MET cc_start: 0.8930 (mmm) cc_final: 0.8558 (tpp) REVERT: Y 104 MET cc_start: 0.7836 (ptt) cc_final: 0.7613 (ptt) REVERT: Y 135 ILE cc_start: 0.7536 (mp) cc_final: 0.7018 (mt) REVERT: Y 220 MET cc_start: 0.8541 (ttt) cc_final: 0.8307 (ttp) REVERT: Y 227 VAL cc_start: 0.9045 (t) cc_final: 0.8808 (m) REVERT: 0 69 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7613 (tm-30) REVERT: 0 237 GLN cc_start: 0.8215 (mp10) cc_final: 0.7905 (mp10) REVERT: 0 300 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8008 (ptm160) REVERT: 0 301 THR cc_start: 0.7810 (p) cc_final: 0.7299 (p) REVERT: 0 303 GLU cc_start: 0.7875 (mp0) cc_final: 0.7330 (pm20) REVERT: 1 86 ASP cc_start: 0.8682 (t0) cc_final: 0.8274 (m-30) REVERT: 1 103 SER cc_start: 0.9064 (t) cc_final: 0.8820 (m) REVERT: 1 144 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: 2 183 ASN cc_start: 0.7787 (m-40) cc_final: 0.6704 (t0) REVERT: 3 112 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7089 (mp0) REVERT: 3 173 MET cc_start: 0.9176 (mtm) cc_final: 0.8930 (mtm) REVERT: 4 23 GLU cc_start: 0.3181 (mm-30) cc_final: 0.2807 (mm-30) REVERT: 4 80 GLN cc_start: 0.3044 (OUTLIER) cc_final: 0.2191 (tp40) outliers start: 198 outliers final: 151 residues processed: 804 average time/residue: 0.5853 time to fit residues: 808.7338 Evaluate side-chains 781 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 616 time to evaluate : 5.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 424 ASN Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 697 THR Chi-restraints excluded: chain N residue 703 ARG Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 858 MET Chi-restraints excluded: chain N residue 923 CYS Chi-restraints excluded: chain N residue 950 VAL Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 167 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain P residue 556 ILE Chi-restraints excluded: chain P residue 564 LEU Chi-restraints excluded: chain P residue 685 SER Chi-restraints excluded: chain P residue 716 GLU Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 790 CYS Chi-restraints excluded: chain P residue 794 GLU Chi-restraints excluded: chain P residue 803 CYS Chi-restraints excluded: chain P residue 828 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 245 VAL Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 493 LEU Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 570 THR Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 129 GLN Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 85 MET Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 458 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 674 THR Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 710 THR Chi-restraints excluded: chain W residue 739 LEU Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1158 GLU Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 180 ILE Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 257 THR Chi-restraints excluded: chain X residue 274 GLN Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 819 SER Chi-restraints excluded: chain X residue 830 THR Chi-restraints excluded: chain X residue 952 VAL Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 166 THR Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 0 residue 276 LEU Chi-restraints excluded: chain 0 residue 300 ARG Chi-restraints excluded: chain 1 residue 110 VAL Chi-restraints excluded: chain 1 residue 136 LEU Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 684 optimal weight: 0.7980 chunk 721 optimal weight: 3.9990 chunk 657 optimal weight: 0.3980 chunk 701 optimal weight: 0.9990 chunk 720 optimal weight: 0.8980 chunk 422 optimal weight: 0.5980 chunk 305 optimal weight: 1.9990 chunk 550 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 633 optimal weight: 0.9990 chunk 663 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN G 129 HIS ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 424 ASN ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 ASN ** Q 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 GLN ** W 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 63572 Z= 0.189 Angle : 0.603 12.461 86106 Z= 0.301 Chirality : 0.041 0.273 9878 Planarity : 0.004 0.057 10995 Dihedral : 4.661 89.784 8432 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 2.47 % Allowed : 19.00 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.10), residues: 7758 helix: 2.27 (0.08), residues: 4267 sheet: -0.24 (0.18), residues: 792 loop : -1.73 (0.11), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 4 105 HIS 0.008 0.001 HIS K 58 PHE 0.032 0.001 PHE W 47 TYR 0.032 0.001 TYR 4 51 ARG 0.008 0.000 ARG P 812 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 652 time to evaluate : 5.411 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: A 107 MET cc_start: 0.3857 (tpp) cc_final: 0.3581 (tpp) REVERT: A 361 MET cc_start: 0.7454 (mmm) cc_final: 0.7098 (mtm) REVERT: D 66 LEU cc_start: 0.3505 (OUTLIER) cc_final: 0.3291 (mp) REVERT: D 85 ASN cc_start: 0.4898 (m-40) cc_final: 0.4613 (m-40) REVERT: D 88 LYS cc_start: 0.5389 (mttt) cc_final: 0.5034 (tttm) REVERT: D 108 GLN cc_start: 0.5353 (pt0) cc_final: 0.3773 (mm-40) REVERT: D 180 LEU cc_start: 0.4171 (OUTLIER) cc_final: 0.3871 (pp) REVERT: G 26 ILE cc_start: 0.1724 (tp) cc_final: 0.1503 (tp) REVERT: G 43 MET cc_start: -0.1449 (OUTLIER) cc_final: -0.2178 (pmm) REVERT: G 44 MET cc_start: 0.1867 (ttp) cc_final: 0.1094 (mmt) REVERT: G 114 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.5100 (mt) REVERT: H 158 GLU cc_start: 0.2596 (pp20) cc_final: 0.1065 (mm-30) REVERT: I 104 MET cc_start: 0.2682 (mmp) cc_final: 0.2109 (tpt) REVERT: J 121 MET cc_start: -0.2590 (tpt) cc_final: -0.4288 (ptt) REVERT: K 77 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6674 (mm110) REVERT: K 92 MET cc_start: 0.7612 (mmt) cc_final: 0.7136 (mmt) REVERT: N 117 MET cc_start: -0.0173 (tmm) cc_final: -0.0582 (ptm) REVERT: N 227 GLU cc_start: 0.7296 (mp0) cc_final: 0.6856 (mp0) REVERT: N 305 LEU cc_start: 0.8416 (mt) cc_final: 0.7925 (tt) REVERT: N 450 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7258 (mt-10) REVERT: N 547 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7370 (pt0) REVERT: N 674 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7491 (tm-30) REVERT: N 830 LYS cc_start: 0.7757 (mttt) cc_final: 0.7201 (mtmm) REVERT: O 681 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7731 (mt-10) REVERT: O 714 ASP cc_start: 0.8147 (m-30) cc_final: 0.7454 (t0) REVERT: O 739 ARG cc_start: 0.7805 (mmt90) cc_final: 0.7578 (mmt90) REVERT: O 766 LYS cc_start: 0.8453 (mttt) cc_final: 0.8210 (mmtp) REVERT: P 100 ASP cc_start: 0.8617 (p0) cc_final: 0.8303 (p0) REVERT: P 247 SER cc_start: 0.8865 (t) cc_final: 0.8625 (m) REVERT: Q 264 GLN cc_start: 0.6143 (tm-30) cc_final: 0.5684 (mp10) REVERT: Q 415 LYS cc_start: 0.7965 (mttt) cc_final: 0.7376 (tptp) REVERT: Q 478 LEU cc_start: 0.8408 (mp) cc_final: 0.8071 (tt) REVERT: Q 493 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8940 (mp) REVERT: R 119 MET cc_start: 0.7431 (mmm) cc_final: 0.7210 (ptt) REVERT: R 191 GLU cc_start: 0.7196 (pt0) cc_final: 0.6800 (mm-30) REVERT: R 201 LYS cc_start: 0.6008 (ttpt) cc_final: 0.4829 (pptt) REVERT: T 1 MET cc_start: 0.6283 (ptp) cc_final: 0.5634 (ptp) REVERT: T 81 ASN cc_start: 0.8100 (t0) cc_final: 0.7523 (t0) REVERT: T 99 LYS cc_start: 0.4840 (OUTLIER) cc_final: 0.4565 (pttm) REVERT: T 153 CYS cc_start: 0.7915 (p) cc_final: 0.7583 (p) REVERT: U 61 LEU cc_start: 0.1980 (tp) cc_final: 0.0605 (pp) REVERT: V 30 MET cc_start: 0.4303 (mmp) cc_final: 0.2707 (tmm) REVERT: V 103 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7404 (tm-30) REVERT: V 126 ASP cc_start: 0.7829 (t0) cc_final: 0.7373 (t0) REVERT: V 129 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7253 (mp0) REVERT: W 20 GLU cc_start: 0.6837 (mp0) cc_final: 0.6566 (mp0) REVERT: W 37 LEU cc_start: 0.8513 (mt) cc_final: 0.8247 (mt) REVERT: W 310 TYR cc_start: 0.8411 (t80) cc_final: 0.8198 (t80) REVERT: W 343 LEU cc_start: 0.8654 (tt) cc_final: 0.8363 (mp) REVERT: W 373 MET cc_start: 0.8722 (mmm) cc_final: 0.8311 (mmm) REVERT: W 396 MET cc_start: 0.8894 (mtt) cc_final: 0.8441 (mtp) REVERT: W 495 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6856 (pt) REVERT: W 739 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8463 (mp) REVERT: W 976 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7576 (mt-10) REVERT: W 1012 TYR cc_start: 0.8703 (m-80) cc_final: 0.8390 (m-80) REVERT: W 1014 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7550 (tmm) REVERT: W 1158 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: W 1203 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6685 (tpt) REVERT: W 1277 MET cc_start: 0.8746 (mtt) cc_final: 0.8399 (mtp) REVERT: X 223 ARG cc_start: 0.8206 (mtt180) cc_final: 0.7560 (mmm160) REVERT: X 420 ILE cc_start: 0.7498 (mm) cc_final: 0.7277 (mt) REVERT: X 499 MET cc_start: 0.7514 (mtp) cc_final: 0.7172 (mtp) REVERT: X 580 SER cc_start: 0.8919 (m) cc_final: 0.8294 (p) REVERT: X 676 ASP cc_start: 0.7813 (p0) cc_final: 0.7586 (p0) REVERT: X 835 ARG cc_start: 0.7305 (ttp-110) cc_final: 0.7088 (tmm-80) REVERT: X 893 MET cc_start: 0.8934 (mmm) cc_final: 0.8576 (tpp) REVERT: Y 104 MET cc_start: 0.7867 (ptt) cc_final: 0.7666 (ptt) REVERT: Y 135 ILE cc_start: 0.7492 (mp) cc_final: 0.6984 (mt) REVERT: Y 220 MET cc_start: 0.8511 (ttt) cc_final: 0.8272 (ttp) REVERT: Y 227 VAL cc_start: 0.9036 (t) cc_final: 0.8803 (m) REVERT: 0 69 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7600 (tm-30) REVERT: 0 237 GLN cc_start: 0.8202 (mp10) cc_final: 0.7866 (mp10) REVERT: 0 300 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8002 (ptm160) REVERT: 0 301 THR cc_start: 0.7850 (p) cc_final: 0.7334 (p) REVERT: 0 303 GLU cc_start: 0.7874 (mp0) cc_final: 0.7354 (pm20) REVERT: 1 86 ASP cc_start: 0.8673 (t0) cc_final: 0.8251 (m-30) REVERT: 1 103 SER cc_start: 0.9056 (t) cc_final: 0.8816 (m) REVERT: 1 144 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: 2 89 ASP cc_start: 0.7869 (m-30) cc_final: 0.7634 (m-30) REVERT: 2 126 CYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7574 (m) REVERT: 2 183 ASN cc_start: 0.7725 (m-40) cc_final: 0.6643 (t0) REVERT: 3 112 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7036 (mp0) REVERT: 3 173 MET cc_start: 0.9168 (mtm) cc_final: 0.8932 (mtm) REVERT: 4 23 GLU cc_start: 0.3075 (mm-30) cc_final: 0.0030 (tt0) REVERT: 4 80 GLN cc_start: 0.3121 (OUTLIER) cc_final: 0.2296 (tp40) outliers start: 169 outliers final: 137 residues processed: 786 average time/residue: 0.5526 time to fit residues: 757.7564 Evaluate side-chains 767 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 614 time to evaluate : 5.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 424 ASN Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 697 THR Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 858 MET Chi-restraints excluded: chain N residue 923 CYS Chi-restraints excluded: chain N residue 950 VAL Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain N residue 965 MET Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 397 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain P residue 457 LEU Chi-restraints excluded: chain P residue 556 ILE Chi-restraints excluded: chain P residue 564 LEU Chi-restraints excluded: chain P residue 608 MET Chi-restraints excluded: chain P residue 685 SER Chi-restraints excluded: chain P residue 716 GLU Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 790 CYS Chi-restraints excluded: chain P residue 794 GLU Chi-restraints excluded: chain P residue 803 CYS Chi-restraints excluded: chain P residue 828 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 245 VAL Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 493 LEU Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 570 THR Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 99 LYS Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 85 MET Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 458 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 674 THR Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 710 THR Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 739 LEU Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1158 GLU Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain W residue 1203 MET Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 180 ILE Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 257 THR Chi-restraints excluded: chain X residue 274 GLN Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 830 THR Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 0 residue 276 LEU Chi-restraints excluded: chain 0 residue 300 ARG Chi-restraints excluded: chain 1 residue 110 VAL Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 699 optimal weight: 0.8980 chunk 460 optimal weight: 0.0980 chunk 741 optimal weight: 0.9980 chunk 452 optimal weight: 9.9990 chunk 351 optimal weight: 0.6980 chunk 515 optimal weight: 5.9990 chunk 778 optimal weight: 3.9990 chunk 716 optimal weight: 0.7980 chunk 619 optimal weight: 0.5980 chunk 64 optimal weight: 0.0170 chunk 478 optimal weight: 0.9980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 ASN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 ASN ** P 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 567 HIS Q 367 HIS Q 611 GLN R 99 HIS ** U 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 628 HIS ** W 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 564 ASN ** 2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 63572 Z= 0.175 Angle : 0.598 12.026 86106 Z= 0.298 Chirality : 0.041 0.267 9878 Planarity : 0.004 0.070 10995 Dihedral : 4.574 89.031 8432 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 2.39 % Allowed : 19.24 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.10), residues: 7758 helix: 2.35 (0.08), residues: 4261 sheet: -0.19 (0.18), residues: 797 loop : -1.69 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 4 105 HIS 0.008 0.001 HIS K 58 PHE 0.028 0.001 PHE N 423 TYR 0.021 0.001 TYR W 808 ARG 0.007 0.000 ARG N 737 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 648 time to evaluate : 5.323 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: A 107 MET cc_start: 0.3873 (tpp) cc_final: 0.3619 (tpp) REVERT: D 66 LEU cc_start: 0.3515 (OUTLIER) cc_final: 0.3297 (mp) REVERT: D 85 ASN cc_start: 0.4887 (m-40) cc_final: 0.4577 (m-40) REVERT: D 88 LYS cc_start: 0.5367 (mttt) cc_final: 0.5026 (tttm) REVERT: D 108 GLN cc_start: 0.5243 (pt0) cc_final: 0.3799 (mm-40) REVERT: D 180 LEU cc_start: 0.4624 (OUTLIER) cc_final: 0.4200 (pp) REVERT: G 26 ILE cc_start: 0.1716 (tp) cc_final: 0.1507 (tp) REVERT: G 43 MET cc_start: -0.1433 (OUTLIER) cc_final: -0.2123 (pmm) REVERT: G 44 MET cc_start: 0.1733 (ttp) cc_final: 0.1154 (mmt) REVERT: G 114 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.5021 (mt) REVERT: H 158 GLU cc_start: 0.2797 (pp20) cc_final: 0.1162 (mm-30) REVERT: I 104 MET cc_start: 0.2962 (mmp) cc_final: 0.2241 (tpt) REVERT: J 121 MET cc_start: -0.2583 (tpt) cc_final: -0.4283 (ptt) REVERT: K 77 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6710 (mm110) REVERT: K 92 MET cc_start: 0.7592 (mmt) cc_final: 0.7121 (mmt) REVERT: N 117 MET cc_start: -0.0173 (tmm) cc_final: -0.0583 (ptm) REVERT: N 227 GLU cc_start: 0.7309 (mp0) cc_final: 0.6875 (mp0) REVERT: N 305 LEU cc_start: 0.8376 (mt) cc_final: 0.7872 (tt) REVERT: N 450 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7125 (mt-10) REVERT: N 525 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6153 (m-80) REVERT: N 547 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7325 (pt0) REVERT: N 674 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7474 (tm-30) REVERT: N 830 LYS cc_start: 0.7745 (mttt) cc_final: 0.7188 (mtmm) REVERT: O 681 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7731 (mt-10) REVERT: O 697 HIS cc_start: 0.6407 (m90) cc_final: 0.6085 (m90) REVERT: O 739 ARG cc_start: 0.7785 (mmt90) cc_final: 0.7557 (mmt90) REVERT: O 766 LYS cc_start: 0.8439 (mttt) cc_final: 0.8206 (mmtp) REVERT: P 100 ASP cc_start: 0.8579 (p0) cc_final: 0.8293 (p0) REVERT: P 112 ASP cc_start: 0.8205 (m-30) cc_final: 0.7347 (t0) REVERT: P 170 LEU cc_start: 0.8614 (pt) cc_final: 0.7717 (tp) REVERT: P 247 SER cc_start: 0.8870 (t) cc_final: 0.8633 (m) REVERT: Q 264 GLN cc_start: 0.6187 (tm-30) cc_final: 0.5655 (mp10) REVERT: Q 415 LYS cc_start: 0.7912 (mttt) cc_final: 0.7348 (tptp) REVERT: Q 478 LEU cc_start: 0.8398 (mp) cc_final: 0.8073 (tt) REVERT: Q 493 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8938 (mp) REVERT: R 119 MET cc_start: 0.7429 (mmm) cc_final: 0.7210 (ptt) REVERT: R 191 GLU cc_start: 0.7070 (pt0) cc_final: 0.6756 (mm-30) REVERT: R 201 LYS cc_start: 0.6184 (ttpt) cc_final: 0.4890 (pptt) REVERT: T 1 MET cc_start: 0.6489 (ptp) cc_final: 0.5844 (ptp) REVERT: T 81 ASN cc_start: 0.8055 (t0) cc_final: 0.7498 (t0) REVERT: T 99 LYS cc_start: 0.4894 (OUTLIER) cc_final: 0.4564 (pttm) REVERT: T 153 CYS cc_start: 0.7905 (p) cc_final: 0.7569 (p) REVERT: U 61 LEU cc_start: 0.2151 (tp) cc_final: 0.0754 (pp) REVERT: V 30 MET cc_start: 0.4212 (mmp) cc_final: 0.2769 (tmm) REVERT: V 129 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7271 (mp0) REVERT: W 19 GLU cc_start: 0.6552 (tp30) cc_final: 0.6212 (tp30) REVERT: W 37 LEU cc_start: 0.8519 (mt) cc_final: 0.8258 (mt) REVERT: W 343 LEU cc_start: 0.8676 (tt) cc_final: 0.8366 (mp) REVERT: W 373 MET cc_start: 0.8704 (mmm) cc_final: 0.8375 (mmm) REVERT: W 396 MET cc_start: 0.8895 (mtt) cc_final: 0.8552 (mtp) REVERT: W 495 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6740 (pt) REVERT: W 739 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8440 (mp) REVERT: W 796 MET cc_start: 0.8183 (ppp) cc_final: 0.7972 (ppp) REVERT: W 976 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7502 (mt-10) REVERT: W 1012 TYR cc_start: 0.8678 (m-80) cc_final: 0.8325 (m-80) REVERT: W 1014 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7507 (tmm) REVERT: W 1158 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: W 1277 MET cc_start: 0.8746 (mtt) cc_final: 0.8403 (mtp) REVERT: X 189 TRP cc_start: 0.6310 (OUTLIER) cc_final: 0.5635 (t60) REVERT: X 223 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7648 (mmm160) REVERT: X 420 ILE cc_start: 0.7500 (mm) cc_final: 0.7284 (mt) REVERT: X 499 MET cc_start: 0.7493 (mtp) cc_final: 0.7153 (mtp) REVERT: X 580 SER cc_start: 0.8943 (m) cc_final: 0.8336 (p) REVERT: X 676 ASP cc_start: 0.7797 (p0) cc_final: 0.7588 (p0) REVERT: X 893 MET cc_start: 0.8908 (mmm) cc_final: 0.8535 (tpp) REVERT: Y 104 MET cc_start: 0.7892 (ptt) cc_final: 0.7686 (ptp) REVERT: Y 135 ILE cc_start: 0.7497 (mp) cc_final: 0.6986 (mt) REVERT: Y 220 MET cc_start: 0.8485 (ttt) cc_final: 0.8261 (ttp) REVERT: Y 227 VAL cc_start: 0.9027 (t) cc_final: 0.8793 (m) REVERT: 0 69 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7622 (tm-30) REVERT: 0 237 GLN cc_start: 0.8190 (mp10) cc_final: 0.7858 (mp10) REVERT: 0 300 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7976 (ptm160) REVERT: 0 301 THR cc_start: 0.7917 (p) cc_final: 0.7381 (p) REVERT: 0 303 GLU cc_start: 0.7888 (mp0) cc_final: 0.7339 (pm20) REVERT: 1 86 ASP cc_start: 0.8698 (t0) cc_final: 0.8277 (m-30) REVERT: 1 103 SER cc_start: 0.9044 (t) cc_final: 0.8809 (m) REVERT: 1 144 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: 2 68 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7726 (mmmt) REVERT: 2 89 ASP cc_start: 0.7866 (m-30) cc_final: 0.7565 (m-30) REVERT: 2 126 CYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7630 (m) REVERT: 2 183 ASN cc_start: 0.7692 (m-40) cc_final: 0.6588 (t0) REVERT: 3 112 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7035 (mp0) REVERT: 3 173 MET cc_start: 0.9149 (mtm) cc_final: 0.8891 (mtm) REVERT: 4 23 GLU cc_start: 0.2933 (mm-30) cc_final: 0.0057 (tt0) REVERT: 4 80 GLN cc_start: 0.2903 (OUTLIER) cc_final: 0.2354 (tp40) REVERT: 4 105 TRP cc_start: 0.1516 (OUTLIER) cc_final: 0.1015 (t60) outliers start: 164 outliers final: 127 residues processed: 779 average time/residue: 0.5520 time to fit residues: 750.3151 Evaluate side-chains 763 residues out of total 7070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 618 time to evaluate : 5.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 424 ASN Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 697 THR Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 858 MET Chi-restraints excluded: chain N residue 923 CYS Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain N residue 965 MET Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 397 LEU Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain P residue 556 ILE Chi-restraints excluded: chain P residue 564 LEU Chi-restraints excluded: chain P residue 685 SER Chi-restraints excluded: chain P residue 716 GLU Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 790 CYS Chi-restraints excluded: chain P residue 794 GLU Chi-restraints excluded: chain P residue 803 CYS Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 245 VAL Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 493 LEU Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 570 THR Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 99 LYS Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 85 MET Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 458 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 643 LEU Chi-restraints excluded: chain W residue 674 THR Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 710 THR Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 739 LEU Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 885 ILE Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1158 GLU Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 180 ILE Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 257 THR Chi-restraints excluded: chain X residue 274 GLN Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 830 THR Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 276 LEU Chi-restraints excluded: chain 0 residue 300 ARG Chi-restraints excluded: chain 1 residue 110 VAL Chi-restraints excluded: chain 1 residue 136 LEU Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 379 optimal weight: 0.9980 chunk 492 optimal weight: 0.6980 chunk 660 optimal weight: 0.9980 chunk 189 optimal weight: 0.0050 chunk 571 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 620 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 637 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 426 ASN ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 ASN U 129 GLN ** W 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 163 GLN ** 2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.164068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119584 restraints weight = 129102.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113739 restraints weight = 89354.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114228 restraints weight = 86382.820| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 63572 Z= 0.204 Angle : 0.609 12.080 86106 Z= 0.304 Chirality : 0.041 0.265 9878 Planarity : 0.004 0.065 10995 Dihedral : 4.582 88.185 8431 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 2.42 % Allowed : 19.52 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.10), residues: 7758 helix: 2.35 (0.08), residues: 4263 sheet: -0.18 (0.18), residues: 803 loop : -1.67 (0.12), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 4 105 HIS 0.008 0.001 HIS K 58 PHE 0.049 0.001 PHE W 789 TYR 0.025 0.001 TYR 4 51 ARG 0.006 0.000 ARG P 812 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14820.57 seconds wall clock time: 260 minutes 30.45 seconds (15630.45 seconds total)