Starting phenix.real_space_refine on Mon Aug 10 03:15:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p4c_17405/08_2026/8p4c_17405.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4c_17405/08_2026/8p4c_17405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p4c_17405/08_2026/8p4c_17405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4c_17405/08_2026/8p4c_17405.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8p4c_17405/08_2026/8p4c_17405.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p4c_17405/08_2026/8p4c_17405.cif" model { file = "/net/cci-nas-00/data/ceres_data/8p4c_17405/08_2026/8p4c_17405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4c_17405/08_2026/8p4c_17405.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.005 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 248 5.16 5 C 25912 2.51 5 N 7276 2.21 5 O 7909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41439 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11166 Classifications: {'peptide': 1410} Link IDs: {'PCIS': 1, 'PTRANS': 68, 'TRANS': 1340} Chain breaks: 5 Chain: "M" Number of atoms: 3958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3958 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 466} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "T" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 847 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "B" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 9052 Classifications: {'peptide': 1132} Link IDs: {'PTRANS': 53, 'TRANS': 1078} Chain breaks: 4 Chain: "C" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2115 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 15, 'TRANS': 247} Chain breaks: 1 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 949 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "P" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 368 Classifications: {'RNAv2': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "D" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3676 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 17, 'TRANS': 440} Chain breaks: 7 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" 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 464 SG CYS A 71 67.597 106.007 96.878 1.00 99.80 S ATOM 486 SG CYS A 74 71.539 106.013 96.131 1.00 95.82 S ATOM 768 SG CYS A 111 81.212 116.736 141.941 1.00132.71 S ATOM 796 SG CYS A 114 80.810 118.329 140.849 1.00130.87 S ATOM 36967 SG CYS Y 16 24.446 129.179 133.123 1.00 81.24 S ATOM 36989 SG CYS Y 19 25.411 127.429 136.957 1.00 84.47 S ATOM 37101 SG CYS Y 33 21.711 127.569 136.314 1.00 73.71 S Time building chain proxies: 8.28, per 1000 atoms: 0.20 Number of scatterers: 41439 At special positions: 0 Unit cell: (158.55, 166.95, 202.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 248 16.00 P 90 15.00 Mg 1 11.99 O 7909 8.00 N 7276 7.00 C 25912 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 Atom "ATOM 15309 O5' DA N 24 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9304 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 57 sheets defined 34.8% alpha, 18.5% beta 39 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 4.79 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.605A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.008A pdb=" N ARG A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.616A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.860A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.857A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.285A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.534A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 696 through 722 removed outlier: 3.687A pdb=" N GLN A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.732A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.539A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.520A pdb=" N GLU A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 932 removed outlier: 3.736A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.664A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.690A pdb=" N GLU A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.539A pdb=" N GLU A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.630A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.103A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1188 through 1195 Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1282 through 1295 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.560A pdb=" N VAL A1385 " --> pdb=" O GLU A1381 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.849A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1436 through 1446 Processing helix chain 'A' and resid 1454 through 1460 removed outlier: 3.749A pdb=" N MET A1459 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.526A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 36 Processing helix chain 'M' and resid 40 through 44 Processing helix chain 'M' and resid 46 through 57 removed outlier: 3.676A pdb=" N LEU M 50 " --> pdb=" O HIS M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 81 Processing helix chain 'M' and resid 99 through 117 removed outlier: 3.791A pdb=" N ARG M 116 " --> pdb=" O ARG M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 146 Processing helix chain 'M' and resid 148 through 160 Processing helix chain 'M' and resid 166 through 178 Processing helix chain 'M' and resid 246 through 262 removed outlier: 3.860A pdb=" N GLU M 252 " --> pdb=" O PRO M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 281 No H-bonds generated for 'chain 'M' and resid 279 through 281' Processing helix chain 'M' and resid 282 through 287 removed outlier: 3.595A pdb=" N LEU M 286 " --> pdb=" O LYS M 282 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS M 287 " --> pdb=" O LEU M 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 282 through 287' Processing helix chain 'M' and resid 371 through 375 Processing helix chain 'M' and resid 376 through 388 Processing helix chain 'M' and resid 388 through 398 removed outlier: 3.671A pdb=" N ARG M 392 " --> pdb=" O ILE M 388 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR M 398 " --> pdb=" O GLU M 394 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 406 removed outlier: 3.588A pdb=" N GLU M 406 " --> pdb=" O LYS M 403 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 424 removed outlier: 3.860A pdb=" N ARG M 422 " --> pdb=" O ILE M 418 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS M 423 " --> pdb=" O CYS M 419 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU M 424 " --> pdb=" O THR M 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 418 through 424' Processing helix chain 'M' and resid 504 through 508 Processing helix chain 'M' and resid 538 through 551 Processing helix chain 'M' and resid 554 through 564 removed outlier: 3.829A pdb=" N GLU M 560 " --> pdb=" O GLU M 556 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE M 561 " --> pdb=" O MET M 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.464A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.427A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 281 through 287 removed outlier: 3.534A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.713A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.526A pdb=" N ALA B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.660A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.944A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.583A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 583 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.827A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 707 through 711 removed outlier: 3.842A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 711' Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.643A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 804 Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.834A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.529A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.621A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.646A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.664A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.868A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.589A pdb=" N PHE E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 removed outlier: 3.889A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 133 through 137 removed outlier: 4.253A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.965A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.534A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.512A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.840A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.794A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.545A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.717A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.444A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.640A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.759A pdb=" N LEU D 97 " --> pdb=" O HIS D 93 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.791A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 removed outlier: 3.642A pdb=" N VAL Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 231 through 239 removed outlier: 3.655A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 245 through 249 removed outlier: 3.563A pdb=" N TYR Z 249 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 removed outlier: 3.718A pdb=" N MET Z 260 " --> pdb=" O ILE Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 349 Processing helix chain 'Z' and resid 464 through 466 No H-bonds generated for 'chain 'Z' and resid 464 through 466' Processing helix chain 'Z' and resid 630 through 633 removed outlier: 4.185A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.690A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 10.669A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 369 removed outlier: 3.710A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 459 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.771A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.208A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.208A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 603 removed outlier: 3.610A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id=AB6, first strand: chain 'A' and resid 1245 through 1247 removed outlier: 3.616A pdb=" N LEU A1257 " --> pdb=" O VAL A1214 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1214 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AB8, first strand: chain 'M' and resid 24 through 27 removed outlier: 5.942A pdb=" N LEU M 121 " --> pdb=" O MET M 61 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU M 63 " --> pdb=" O LEU M 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 242 through 243 removed outlier: 7.268A pdb=" N LEU M 341 " --> pdb=" O ILE M 364 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE M 364 " --> pdb=" O LEU M 341 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP M 343 " --> pdb=" O TYR M 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 272 through 275 removed outlier: 10.069A pdb=" N GLN M 272 " --> pdb=" O ASP M 454 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE M 456 " --> pdb=" O GLN M 272 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N ASP M 455 " --> pdb=" O PRO M 444 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 494 through 501 removed outlier: 7.285A pdb=" N VAL M 491 " --> pdb=" O PRO M 497 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY M 487 " --> pdb=" O ILE M 501 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE M 514 " --> pdb=" O GLN M 529 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN M 529 " --> pdb=" O ILE M 514 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLU M 516 " --> pdb=" O MET M 527 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 87 through 93 removed outlier: 4.933A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP B 127 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AC5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC7, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.557A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD1, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.546A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.588A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR L 17 " --> pdb=" O ASN L 26 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD4, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.152A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD6, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.790A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id=AD8, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.464A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 44 through 55 removed outlier: 5.165A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.421A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.516A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE5, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE6, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'D' and resid 30 through 31 removed outlier: 6.056A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AF2, first strand: chain 'G' and resid 83 through 92 removed outlier: 6.612A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 147 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AF4, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF5, first strand: chain 'Y' and resid 83 through 90 removed outlier: 7.116A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE Y 60 " --> pdb=" O ALA Z 217 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 352 through 355 removed outlier: 3.996A pdb=" N PHE Z 358 " --> pdb=" O ASP Z 355 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR Z 366 " --> pdb=" O PHE Z 373 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'Z' and resid 477 through 479 removed outlier: 5.843A pdb=" N ILE Z 492 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE Z 503 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG Z 494 " --> pdb=" O ILE Z 501 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.494A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR Z 546 " --> pdb=" O LEU Z 542 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 586 through 587 Processing sheet with id=AG2, first strand: chain 'Z' and resid 635 through 639 removed outlier: 6.657A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Z' and resid 742 through 746 removed outlier: 6.954A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) 1547 hydrogen bonds defined for protein. 4293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 13.49 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8024 1.33 - 1.45: 10280 1.45 - 1.57: 23537 1.57 - 1.70: 179 1.70 - 1.82: 392 Bond restraints: 42412 Sorted by residual: bond pdb=" CA ILE Z 450 " pdb=" C ILE Z 450 " ideal model delta sigma weight residual 1.522 1.448 0.074 1.16e-02 7.43e+03 4.11e+01 bond pdb=" CA THR Z 449 " pdb=" C THR Z 449 " ideal model delta sigma weight residual 1.530 1.460 0.070 1.17e-02 7.31e+03 3.57e+01 bond pdb=" N ILE Z 450 " pdb=" CA ILE Z 450 " ideal model delta sigma weight residual 1.458 1.402 0.057 1.20e-02 6.94e+03 2.23e+01 bond pdb=" CA LYS Z 447 " pdb=" C LYS Z 447 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.29e-02 6.01e+03 2.08e+01 bond pdb=" CA ILE Z 448 " pdb=" C ILE Z 448 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.30e-02 5.92e+03 1.93e+01 ... (remaining 42407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 57087 3.37 - 6.73: 507 6.73 - 10.10: 45 10.10 - 13.46: 7 13.46 - 16.83: 2 Bond angle restraints: 57648 Sorted by residual: angle pdb=" N THR Z 449 " pdb=" CA THR Z 449 " pdb=" C THR Z 449 " ideal model delta sigma weight residual 111.28 94.45 16.83 1.35e+00 5.49e-01 1.55e+02 angle pdb=" C LYS M 449 " pdb=" N PRO M 450 " pdb=" CA PRO M 450 " ideal model delta sigma weight residual 120.21 131.08 -10.87 9.60e-01 1.09e+00 1.28e+02 angle pdb=" N ILE Z 450 " pdb=" CA ILE Z 450 " pdb=" C ILE Z 450 " ideal model delta sigma weight residual 109.21 94.16 15.05 1.36e+00 5.41e-01 1.22e+02 angle pdb=" N GLY Z 423 " pdb=" CA GLY Z 423 " pdb=" C GLY Z 423 " ideal model delta sigma weight residual 114.69 127.01 -12.32 1.19e+00 7.06e-01 1.07e+02 angle pdb=" N LYS Z 447 " pdb=" CA LYS Z 447 " pdb=" C LYS Z 447 " ideal model delta sigma weight residual 109.15 96.46 12.69 1.44e+00 4.82e-01 7.77e+01 ... (remaining 57643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 24933 35.01 - 70.01: 733 70.01 - 105.02: 42 105.02 - 140.02: 0 140.02 - 175.03: 4 Dihedral angle restraints: 25712 sinusoidal: 11331 harmonic: 14381 Sorted by residual: dihedral pdb=" C4' C P 30 " pdb=" C3' C P 30 " pdb=" C2' C P 30 " pdb=" C1' C P 30 " ideal model delta sinusoidal sigma weight residual 36.34 -37.53 73.88 1 3.10e+00 1.04e-01 7.22e+02 dihedral pdb=" C4' A P 35 " pdb=" C3' A P 35 " pdb=" C2' A P 35 " pdb=" C1' A P 35 " ideal model delta sinusoidal sigma weight residual 36.35 -36.87 73.21 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' G P 36 " pdb=" C3' G P 36 " pdb=" C2' G P 36 " pdb=" C1' G P 36 " ideal model delta sinusoidal sigma weight residual 36.34 -27.49 63.83 1 3.10e+00 1.04e-01 5.58e+02 ... (remaining 25709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 6238 0.123 - 0.246: 172 0.246 - 0.369: 19 0.369 - 0.493: 3 0.493 - 0.616: 3 Chirality restraints: 6435 Sorted by residual: chirality pdb=" CA TYR M 362 " pdb=" N TYR M 362 " pdb=" C TYR M 362 " pdb=" CB TYR M 362 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.48e+00 chirality pdb=" CA ASN M 324 " pdb=" N ASN M 324 " pdb=" C ASN M 324 " pdb=" CB ASN M 324 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.48e+00 chirality pdb=" CA TRP M 293 " pdb=" N TRP M 293 " pdb=" C TRP M 293 " pdb=" CB TRP M 293 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.14e+00 ... (remaining 6432 not shown) Planarity restraints: 7144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 74 " 0.059 2.00e-02 2.50e+03 4.14e-02 3.42e+01 pdb=" CG TYR M 74 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR M 74 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR M 74 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR M 74 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR M 74 " -0.043 2.00e-02 2.50e+03 pdb=" CZ TYR M 74 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR M 74 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 35 " -0.059 2.00e-02 2.50e+03 4.03e-02 3.25e+01 pdb=" CG TYR M 35 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR M 35 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR M 35 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR M 35 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR M 35 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR M 35 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR M 35 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 120 " -0.089 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO G 121 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO G 121 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO G 121 " -0.070 5.00e-02 4.00e+02 ... (remaining 7141 not shown) Histogram of nonbonded interaction distances: 0.32 - 1.23: 58 1.23 - 2.15: 261 2.15 - 3.07: 27876 3.07 - 3.98: 113346 3.98 - 4.90: 207694 Warning: very small nonbonded interaction distances. Nonbonded interactions: 349235 Sorted by model distance: nonbonded pdb=" CZ ARG G 151 " pdb=" O ASP Z 505 " model vdw 0.317 3.270 nonbonded pdb=" O PRO M 461 " pdb=" N ASN M 465 " model vdw 0.346 3.120 nonbonded pdb=" CA MET Z 563 " pdb=" CE1 PHE Z 623 " model vdw 0.373 3.770 nonbonded pdb=" CG MET Z 563 " pdb=" CE2 PHE Z 623 " model vdw 0.384 3.740 nonbonded pdb=" CB PHE Z 499 " pdb=" CG ARG Z 555 " model vdw 0.430 3.840 ... (remaining 349230 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=0.65 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.760 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 50.480 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 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 : 0.008 0.819 42424 Z= 0.671 Angle : 0.858 16.828 57648 Z= 0.536 Chirality : 0.056 0.616 6435 Planarity : 0.006 0.134 7144 Dihedral : 14.989 175.030 16408 Min Nonbonded Distance : 0.317 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.84 % Rotamer: Outliers : 0.43 % Allowed : 1.17 % Favored : 98.40 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.11), residues: 4882 helix: 0.00 (0.13), residues: 1526 sheet: -1.05 (0.18), residues: 710 loop : -1.19 (0.11), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 176 TYR 0.078 0.003 TYR M 74 PHE 0.061 0.003 PHE M 113 TRP 0.034 0.003 TRP M 147 HIS 0.015 0.001 HIS M 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.33 (42412) covalent geometry : angle 0.85843 / 0.54 (57648) hydrogen bonds : bond 0.17800 / 11.96 ( 1625) hydrogen bonds : angle 7.29455 / 5.15 ( 4483) metal coordination : bond 0.13650 / 9.49 ( 8) Misc. bond : bond 0.60099 / 30.36 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 616 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 SER cc_start: 0.9109 (m) cc_final: 0.8327 (p) REVERT: A 1086 MET cc_start: 0.8548 (mmm) cc_final: 0.8307 (mmm) REVERT: M 362 TYR cc_start: -0.3407 (OUTLIER) cc_final: -0.3667 (p90) REVERT: M 437 MET cc_start: 0.1135 (ptp) cc_final: -0.0167 (mmm) REVERT: B 368 MET cc_start: 0.8994 (mtp) cc_final: 0.8636 (ttt) REVERT: B 583 LEU cc_start: 0.8355 (tt) cc_final: 0.8140 (tp) REVERT: B 752 TYR cc_start: 0.7862 (m-10) cc_final: 0.6740 (m-10) REVERT: B 846 ASP cc_start: 0.7105 (p0) cc_final: 0.6880 (p0) REVERT: B 907 VAL cc_start: 0.7604 (t) cc_final: 0.6782 (t) REVERT: B 1159 PHE cc_start: 0.8945 (m-10) cc_final: 0.8696 (m-10) REVERT: C 243 THR cc_start: 0.8148 (t) cc_final: 0.7712 (t) REVERT: E 98 ASN cc_start: 0.7994 (p0) cc_final: 0.7775 (p0) REVERT: I 29 ASP cc_start: 0.8663 (t0) cc_final: 0.8446 (t70) REVERT: I 71 ASP cc_start: 0.7322 (p0) cc_final: 0.7046 (p0) REVERT: G 104 MET cc_start: 0.7836 (tmm) cc_final: 0.7103 (tmm) REVERT: Z 378 MET cc_start: -0.2919 (mtt) cc_final: -0.3638 (mtt) REVERT: Z 460 MET cc_start: 0.7292 (mmt) cc_final: 0.6999 (mmt) outliers start: 19 outliers final: 2 residues processed: 634 average time/residue: 0.2561 time to fit residues: 273.8036 Evaluate side-chains 372 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 369 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 425 LEU Chi-restraints excluded: chain M residue 463 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 40.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 6.9990 chunk 494 optimal weight: 0.0570 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 overall best weight: 2.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 432 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 537 ASN M 547 ASN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B 452 ASN B 518 HIS B 593 GLN B 683 GLN B 725 GLN ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS B1071 ASN B1117 HIS C 51 GLN C 260 GLN L 13 GLN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN Y 12 HIS Y 41 GLN Z 178 ASN Z 559 GLN Z 616 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.081301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.052186 restraints weight = 214958.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053393 restraints weight = 108716.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053956 restraints weight = 70655.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.054615 restraints weight = 56033.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054815 restraints weight = 48202.511| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 42424 Z= 0.228 Angle : 0.844 20.387 57648 Z= 0.436 Chirality : 0.056 1.036 6435 Planarity : 0.006 0.093 7144 Dihedral : 14.827 169.333 6407 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.10 % Favored : 94.76 % Rotamer: Outliers : 1.37 % Allowed : 9.04 % Favored : 89.58 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.12), residues: 4882 helix: 0.35 (0.13), residues: 1526 sheet: -0.80 (0.19), residues: 708 loop : -1.05 (0.12), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG M 564 TYR 0.033 0.002 TYR Z 203 PHE 0.123 0.003 PHE Z 623 TRP 0.032 0.002 TRP M 293 HIS 0.025 0.002 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (42412) covalent geometry : angle 0.84396 / 0.44 (57648) hydrogen bonds : bond 0.05166 / 3.47 ( 1625) hydrogen bonds : angle 5.91401 / 4.20 ( 4483) metal coordination : bond 0.00271 / 0.16 ( 8) Misc. bond : bond 0.02629 / 1.28 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 376 time to evaluate : 1.629 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 520 MET cc_start: 0.9288 (mmm) cc_final: 0.9034 (tpp) REVERT: A 561 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.9024 (mmm) REVERT: A 1086 MET cc_start: 0.8858 (mmm) cc_final: 0.8537 (mmm) REVERT: A 1108 HIS cc_start: 0.6627 (m-70) cc_final: 0.6414 (m90) REVERT: A 1228 MET cc_start: 0.8391 (mmm) cc_final: 0.7931 (mtt) REVERT: A 1427 LEU cc_start: 0.9397 (mt) cc_final: 0.9046 (tp) REVERT: A 1459 MET cc_start: 0.8825 (mtt) cc_final: 0.8266 (mtt) REVERT: M 30 MET cc_start: 0.3243 (ptp) cc_final: 0.2897 (ptp) REVERT: M 61 MET cc_start: 0.6255 (tpp) cc_final: 0.5955 (tpp) REVERT: M 396 MET cc_start: 0.6653 (mtt) cc_final: 0.6453 (mtt) REVERT: M 555 LYS cc_start: 0.5740 (OUTLIER) cc_final: 0.5442 (tptp) REVERT: B 53 MET cc_start: 0.8883 (mpp) cc_final: 0.8445 (mpp) REVERT: B 368 MET cc_start: 0.9448 (mtp) cc_final: 0.9176 (ttt) REVERT: B 394 ASP cc_start: 0.7860 (m-30) cc_final: 0.7452 (m-30) REVERT: B 407 MET cc_start: 0.8496 (ptp) cc_final: 0.8285 (ptm) REVERT: B 667 THR cc_start: 0.9501 (m) cc_final: 0.9239 (p) REVERT: B 816 GLU cc_start: 0.7518 (tp30) cc_final: 0.7124 (tp30) REVERT: B 1172 MET cc_start: 0.8226 (mpp) cc_final: 0.7806 (mpp) REVERT: C 15 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7073 (p) REVERT: H 13 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8834 (mmtm) REVERT: I 71 ASP cc_start: 0.7822 (p0) cc_final: 0.7562 (p0) REVERT: K 38 GLU cc_start: 0.8403 (tp30) cc_final: 0.7792 (tp30) REVERT: K 42 LEU cc_start: 0.9692 (mt) cc_final: 0.9421 (mt) REVERT: K 50 LEU cc_start: 0.9780 (OUTLIER) cc_final: 0.9454 (mt) REVERT: K 102 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8246 (mm-30) REVERT: D 19 GLN cc_start: 0.9406 (pt0) cc_final: 0.9153 (mp10) REVERT: G 104 MET cc_start: 0.8242 (tmm) cc_final: 0.7289 (tmm) REVERT: G 158 PHE cc_start: 0.8439 (m-80) cc_final: 0.8102 (m-80) REVERT: Z 460 MET cc_start: 0.7574 (mmt) cc_final: 0.7317 (mmp) REVERT: Z 546 THR cc_start: -0.2425 (OUTLIER) cc_final: -0.3333 (t) REVERT: Z 563 MET cc_start: 0.0172 (OUTLIER) cc_final: -0.0458 (ptt) outliers start: 60 outliers final: 28 residues processed: 414 average time/residue: 0.2422 time to fit residues: 172.7368 Evaluate side-chains 353 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 319 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 312 MET Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 555 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 546 THR Chi-restraints excluded: chain Z residue 563 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 301 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 302 optimal weight: 0.9990 chunk 491 optimal weight: 6.9990 chunk 148 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 chunk 374 optimal weight: 9.9990 chunk 332 optimal weight: 7.9990 chunk 354 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 ASN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN M 537 ASN B 23 GLN B 52 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN B1071 ASN C 66 HIS ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN G 9 HIS G 60 GLN Z 737 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.078650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.049468 restraints weight = 214632.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050069 restraints weight = 107046.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050786 restraints weight = 68309.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.051255 restraints weight = 52439.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051357 restraints weight = 45218.167| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 42424 Z= 0.231 Angle : 0.736 13.978 57648 Z= 0.388 Chirality : 0.051 0.725 6435 Planarity : 0.005 0.170 7144 Dihedral : 14.574 170.897 6402 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer: Outliers : 2.11 % Allowed : 10.49 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.12), residues: 4882 helix: 0.59 (0.14), residues: 1538 sheet: -0.77 (0.19), residues: 698 loop : -0.94 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG Z 555 TYR 0.026 0.002 TYR Z 203 PHE 0.024 0.002 PHE Z 618 TRP 0.018 0.002 TRP M 293 HIS 0.023 0.001 HIS Z 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (42412) covalent geometry : angle 0.73577 / 0.39 (57648) hydrogen bonds : bond 0.04616 / 3.12 ( 1625) hydrogen bonds : angle 5.56396 / 3.95 ( 4483) metal coordination : bond 0.00198 / 0.12 ( 8) Misc. bond : bond 0.00530 / 0.26 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 321 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.9132 (m-10) cc_final: 0.8797 (m-10) REVERT: A 469 MET cc_start: 0.8773 (mtp) cc_final: 0.8537 (mtp) REVERT: A 520 MET cc_start: 0.9341 (mmm) cc_final: 0.9139 (tpp) REVERT: A 561 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.8986 (mmm) REVERT: A 930 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9445 (tt) REVERT: A 1038 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9015 (p) REVERT: A 1086 MET cc_start: 0.8993 (mmm) cc_final: 0.8690 (mmm) REVERT: A 1228 MET cc_start: 0.8460 (mmm) cc_final: 0.8048 (mtt) REVERT: A 1428 MET cc_start: 0.8611 (tmm) cc_final: 0.8309 (tpp) REVERT: A 1459 MET cc_start: 0.8998 (mtt) cc_final: 0.8718 (mtt) REVERT: M 30 MET cc_start: 0.3167 (ptp) cc_final: 0.2673 (ptp) REVERT: M 61 MET cc_start: 0.6178 (tpp) cc_final: 0.5760 (tpp) REVERT: M 276 MET cc_start: 0.5173 (ttp) cc_final: 0.4609 (ttm) REVERT: M 437 MET cc_start: -0.0658 (mmm) cc_final: -0.1579 (mtt) REVERT: B 368 MET cc_start: 0.9528 (mtp) cc_final: 0.9272 (ttt) REVERT: B 394 ASP cc_start: 0.8398 (m-30) cc_final: 0.8139 (m-30) REVERT: B 407 MET cc_start: 0.8622 (ptp) cc_final: 0.8270 (ptm) REVERT: B 702 MET cc_start: 0.8550 (mmm) cc_final: 0.8306 (mmp) REVERT: B 764 MET cc_start: 0.8334 (mmt) cc_final: 0.8043 (mmt) REVERT: B 816 GLU cc_start: 0.7906 (tp30) cc_final: 0.7493 (tp30) REVERT: C 62 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7669 (tm-30) REVERT: E 94 MET cc_start: 0.8569 (mmm) cc_final: 0.8285 (tpp) REVERT: H 13 LYS cc_start: 0.9309 (mmtt) cc_final: 0.8813 (mmtm) REVERT: I 108 MET cc_start: 0.8333 (mmp) cc_final: 0.7936 (mmp) REVERT: K 38 GLU cc_start: 0.8497 (tp30) cc_final: 0.8142 (tp30) REVERT: K 50 LEU cc_start: 0.9757 (OUTLIER) cc_final: 0.9459 (mt) REVERT: K 102 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8288 (mm-30) REVERT: L 44 MET cc_start: 0.8370 (mmt) cc_final: 0.7702 (mmm) REVERT: G 104 MET cc_start: 0.8210 (tmm) cc_final: 0.7728 (tmm) REVERT: G 158 PHE cc_start: 0.8511 (m-80) cc_final: 0.8170 (m-10) REVERT: Z 378 MET cc_start: 0.0062 (mtt) cc_final: -0.0170 (mmm) REVERT: Z 460 MET cc_start: 0.7648 (mmt) cc_final: 0.7381 (mmt) REVERT: Z 740 CYS cc_start: 0.8932 (p) cc_final: 0.8666 (p) outliers start: 92 outliers final: 42 residues processed: 391 average time/residue: 0.2215 time to fit residues: 149.0908 Evaluate side-chains 334 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain Z residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 200 optimal weight: 4.9990 chunk 338 optimal weight: 9.9990 chunk 426 optimal weight: 10.0000 chunk 337 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 221 optimal weight: 1.9990 chunk 370 optimal weight: 10.0000 chunk 297 optimal weight: 4.9990 chunk 373 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN A1108 HIS M 90 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 631 GLN ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 559 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.077724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047873 restraints weight = 212421.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.049013 restraints weight = 107856.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.049616 restraints weight = 70344.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049829 restraints weight = 55308.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050109 restraints weight = 49556.294| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 42424 Z= 0.196 Angle : 0.685 16.030 57648 Z= 0.355 Chirality : 0.048 0.463 6435 Planarity : 0.005 0.128 7144 Dihedral : 14.462 171.371 6402 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.22 % Favored : 94.72 % Rotamer: Outliers : 2.01 % Allowed : 11.42 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.12), residues: 4882 helix: 0.74 (0.14), residues: 1541 sheet: -0.73 (0.19), residues: 679 loop : -0.85 (0.12), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 555 TYR 0.023 0.002 TYR B1048 PHE 0.025 0.002 PHE G 107 TRP 0.018 0.002 TRP M 293 HIS 0.009 0.001 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (42412) covalent geometry : angle 0.68464 / 0.36 (57648) hydrogen bonds : bond 0.04150 / 2.81 ( 1625) hydrogen bonds : angle 5.38062 / 3.83 ( 4483) metal coordination : bond 0.00244 / 0.12 ( 8) Misc. bond : bond 0.00838 / 0.40 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 301 time to evaluate : 1.679 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: A 417 LYS cc_start: 0.9248 (tttt) cc_final: 0.8858 (tttm) REVERT: A 467 MET cc_start: 0.8850 (mpp) cc_final: 0.8358 (mpp) REVERT: A 469 MET cc_start: 0.8752 (mtp) cc_final: 0.8455 (mtp) REVERT: A 561 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8941 (mmm) REVERT: A 868 MET cc_start: 0.8852 (mtp) cc_final: 0.8601 (mtt) REVERT: A 1038 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8965 (p) REVERT: A 1086 MET cc_start: 0.9006 (mmm) cc_final: 0.8793 (mmm) REVERT: A 1228 MET cc_start: 0.8616 (mmm) cc_final: 0.8079 (mtt) REVERT: A 1459 MET cc_start: 0.9056 (mtt) cc_final: 0.8783 (mtt) REVERT: M 30 MET cc_start: 0.3582 (ptp) cc_final: 0.3070 (ptp) REVERT: M 276 MET cc_start: 0.5140 (ttp) cc_final: 0.4297 (tmm) REVERT: M 312 MET cc_start: -0.1335 (tpt) cc_final: -0.1674 (tpt) REVERT: M 346 MET cc_start: 0.1585 (mmt) cc_final: 0.1336 (mtt) REVERT: M 437 MET cc_start: -0.0573 (mmm) cc_final: -0.1341 (mtt) REVERT: B 239 MET cc_start: 0.8920 (tpp) cc_final: 0.8606 (tpt) REVERT: B 508 MET cc_start: 0.8627 (mpp) cc_final: 0.8383 (mmm) REVERT: B 683 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7258 (tp-100) REVERT: B 816 GLU cc_start: 0.8097 (tp30) cc_final: 0.7696 (tp30) REVERT: E 94 MET cc_start: 0.8662 (mmm) cc_final: 0.8310 (tpp) REVERT: F 94 MET cc_start: 0.7997 (tmm) cc_final: 0.7446 (tmm) REVERT: F 98 LYS cc_start: 0.9345 (mtmt) cc_final: 0.9040 (mtmt) REVERT: H 13 LYS cc_start: 0.9322 (mmtt) cc_final: 0.8817 (mmtm) REVERT: K 38 GLU cc_start: 0.8553 (tp30) cc_final: 0.8228 (tp30) REVERT: K 50 LEU cc_start: 0.9760 (OUTLIER) cc_final: 0.9503 (mt) REVERT: K 102 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8263 (mm-30) REVERT: L 30 SER cc_start: 0.8785 (m) cc_final: 0.8500 (p) REVERT: L 39 CYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6905 (p) REVERT: L 44 MET cc_start: 0.8515 (mmt) cc_final: 0.8132 (mmm) REVERT: G 104 MET cc_start: 0.8299 (tmm) cc_final: 0.7919 (tmm) REVERT: G 158 PHE cc_start: 0.8506 (m-80) cc_final: 0.8232 (m-10) REVERT: Z 378 MET cc_start: 0.0960 (mtt) cc_final: 0.0668 (mmm) REVERT: Z 451 MET cc_start: 0.7792 (mmm) cc_final: 0.7486 (mmm) REVERT: Z 740 CYS cc_start: 0.8929 (p) cc_final: 0.8647 (p) outliers start: 88 outliers final: 48 residues processed: 374 average time/residue: 0.2464 time to fit residues: 158.3566 Evaluate side-chains 326 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 246 THR Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 683 GLN Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 39 CYS Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 493 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 226 optimal weight: 6.9990 chunk 177 optimal weight: 50.0000 chunk 151 optimal weight: 7.9990 chunk 341 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 148 optimal weight: 40.0000 chunk 384 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 415 optimal weight: 0.3980 chunk 287 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1313 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS H 46 GLN ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.078474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.048906 restraints weight = 211604.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049922 restraints weight = 103692.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.050651 restraints weight = 65744.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.051001 restraints weight = 50625.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051321 restraints weight = 44393.819| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 42424 Z= 0.133 Angle : 0.652 13.512 57648 Z= 0.335 Chirality : 0.046 0.402 6435 Planarity : 0.004 0.115 7144 Dihedral : 14.436 173.434 6402 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Rotamer: Outliers : 1.65 % Allowed : 12.29 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.12), residues: 4882 helix: 0.78 (0.14), residues: 1542 sheet: -0.66 (0.19), residues: 689 loop : -0.81 (0.12), residues: 2651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 16 TYR 0.018 0.001 TYR G 3 PHE 0.032 0.001 PHE M 561 TRP 0.014 0.001 TRP M 293 HIS 0.007 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (42412) covalent geometry : angle 0.65222 / 0.33 (57648) hydrogen bonds : bond 0.03928 / 2.68 ( 1625) hydrogen bonds : angle 5.26204 / 3.74 ( 4483) metal coordination : bond 0.00073 / 0.05 ( 8) Misc. bond : bond 0.00745 / 0.36 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 294 time to evaluate : 1.647 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: A 266 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7996 (tmm) REVERT: A 417 LYS cc_start: 0.9290 (tttt) cc_final: 0.8982 (tttm) REVERT: A 469 MET cc_start: 0.8781 (mtp) cc_final: 0.8550 (mtp) REVERT: A 561 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.8941 (mmm) REVERT: A 1038 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8891 (p) REVERT: A 1228 MET cc_start: 0.8436 (mmm) cc_final: 0.8078 (mtt) REVERT: A 1427 LEU cc_start: 0.9453 (mt) cc_final: 0.9095 (tp) REVERT: A 1459 MET cc_start: 0.9050 (mtt) cc_final: 0.8570 (mtt) REVERT: M 30 MET cc_start: 0.3786 (ptp) cc_final: 0.3126 (ptp) REVERT: M 61 MET cc_start: 0.6846 (tpp) cc_final: 0.6621 (tpp) REVERT: M 276 MET cc_start: 0.3829 (ttp) cc_final: 0.2809 (tmm) REVERT: M 437 MET cc_start: -0.0120 (mmm) cc_final: -0.1151 (mtt) REVERT: M 482 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8645 (pp) REVERT: B 508 MET cc_start: 0.8546 (mpp) cc_final: 0.8323 (mmm) REVERT: B 677 MET cc_start: 0.8164 (mmm) cc_final: 0.7941 (tpp) REVERT: B 692 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.8865 (p) REVERT: B 816 GLU cc_start: 0.8128 (tp30) cc_final: 0.7687 (tp30) REVERT: B 840 MET cc_start: 0.6204 (tpp) cc_final: 0.5796 (tpp) REVERT: E 94 MET cc_start: 0.8770 (mmm) cc_final: 0.8358 (tpp) REVERT: F 98 LYS cc_start: 0.9353 (mtmt) cc_final: 0.9102 (mtpp) REVERT: H 13 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8807 (mmtm) REVERT: K 8 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8362 (mm-30) REVERT: K 38 GLU cc_start: 0.8505 (tp30) cc_final: 0.8186 (tp30) REVERT: K 50 LEU cc_start: 0.9738 (OUTLIER) cc_final: 0.9487 (mt) REVERT: K 102 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8246 (mm-30) REVERT: L 30 SER cc_start: 0.8721 (m) cc_final: 0.8426 (p) REVERT: L 44 MET cc_start: 0.8631 (mmt) cc_final: 0.8230 (mmm) REVERT: G 16 ARG cc_start: 0.8606 (ptm-80) cc_final: 0.8291 (ptt90) REVERT: G 104 MET cc_start: 0.8357 (tmm) cc_final: 0.7985 (tmm) REVERT: G 158 PHE cc_start: 0.8509 (m-80) cc_final: 0.8223 (m-10) REVERT: Z 378 MET cc_start: 0.0097 (mtt) cc_final: -0.0167 (mmm) REVERT: Z 508 MET cc_start: 0.5790 (tpt) cc_final: 0.5485 (tpt) REVERT: Z 740 CYS cc_start: 0.8937 (p) cc_final: 0.8631 (p) outliers start: 72 outliers final: 42 residues processed: 353 average time/residue: 0.2399 time to fit residues: 146.3117 Evaluate side-chains 326 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 278 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain Z residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 483 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 426 optimal weight: 8.9990 chunk 143 optimal weight: 40.0000 chunk 174 optimal weight: 0.0370 chunk 210 optimal weight: 3.9990 chunk 185 optimal weight: 20.0000 chunk 423 optimal weight: 20.0000 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN B1049 GLN ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.076767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.047183 restraints weight = 210485.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.048202 restraints weight = 106606.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.048990 restraints weight = 70630.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049385 restraints weight = 55620.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.049565 restraints weight = 48587.096| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 42424 Z= 0.186 Angle : 0.672 20.459 57648 Z= 0.344 Chirality : 0.046 0.355 6435 Planarity : 0.004 0.109 7144 Dihedral : 14.380 174.432 6402 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 2.06 % Allowed : 12.66 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.12), residues: 4882 helix: 0.96 (0.14), residues: 1532 sheet: -0.72 (0.19), residues: 693 loop : -0.78 (0.12), residues: 2657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 555 TYR 0.026 0.001 TYR B 752 PHE 0.019 0.001 PHE A 113 TRP 0.016 0.001 TRP B 22 HIS 0.011 0.001 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (42412) covalent geometry : angle 0.67162 / 0.34 (57648) hydrogen bonds : bond 0.03932 / 2.67 ( 1625) hydrogen bonds : angle 5.16451 / 3.67 ( 4483) metal coordination : bond 0.00212 / 0.11 ( 8) Misc. bond : bond 0.01104 / 0.53 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 280 time to evaluate : 1.612 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: A 322 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8993 (mm) REVERT: A 355 MET cc_start: 0.8993 (mmp) cc_final: 0.8753 (mmp) REVERT: A 417 LYS cc_start: 0.9355 (tttt) cc_final: 0.9013 (tttm) REVERT: A 469 MET cc_start: 0.8818 (mtp) cc_final: 0.8538 (mtp) REVERT: A 561 MET cc_start: 0.9384 (OUTLIER) cc_final: 0.9054 (mtp) REVERT: A 1038 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8910 (p) REVERT: A 1228 MET cc_start: 0.8602 (mmm) cc_final: 0.8035 (mtt) REVERT: A 1459 MET cc_start: 0.9058 (mtt) cc_final: 0.8784 (mtt) REVERT: M 30 MET cc_start: 0.3642 (ptp) cc_final: 0.3042 (ptp) REVERT: M 276 MET cc_start: 0.4267 (ttp) cc_final: 0.3485 (tmm) REVERT: M 437 MET cc_start: -0.0418 (mmm) cc_final: -0.1141 (mtt) REVERT: M 482 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8784 (pp) REVERT: B 677 MET cc_start: 0.8300 (mmm) cc_final: 0.8013 (tpp) REVERT: B 683 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.7049 (tp-100) REVERT: B 692 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.8996 (p) REVERT: B 764 MET cc_start: 0.8382 (mmt) cc_final: 0.8073 (mtt) REVERT: B 816 GLU cc_start: 0.8183 (tp30) cc_final: 0.7763 (tp30) REVERT: B 840 MET cc_start: 0.6548 (tpp) cc_final: 0.6257 (tpp) REVERT: C 15 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8385 (p) REVERT: C 62 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 127 VAL cc_start: 0.8835 (t) cc_final: 0.8456 (p) REVERT: E 94 MET cc_start: 0.8723 (mmm) cc_final: 0.8491 (tpp) REVERT: F 98 LYS cc_start: 0.9362 (mtmt) cc_final: 0.9089 (mtpp) REVERT: H 13 LYS cc_start: 0.9331 (mmtt) cc_final: 0.8809 (mmtm) REVERT: H 92 MET cc_start: 0.8728 (mtp) cc_final: 0.8423 (mtp) REVERT: K 8 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8457 (mm-30) REVERT: K 38 GLU cc_start: 0.8553 (tp30) cc_final: 0.8317 (tp30) REVERT: K 50 LEU cc_start: 0.9758 (OUTLIER) cc_final: 0.9513 (mt) REVERT: L 30 SER cc_start: 0.8763 (m) cc_final: 0.8507 (p) REVERT: L 44 MET cc_start: 0.8794 (mmt) cc_final: 0.8442 (mmm) REVERT: L 56 ASP cc_start: 0.8202 (t0) cc_final: 0.7838 (t0) REVERT: D 62 MET cc_start: 0.9157 (mmm) cc_final: 0.8949 (mpp) REVERT: G 104 MET cc_start: 0.8309 (tmm) cc_final: 0.7947 (tmm) REVERT: G 118 GLU cc_start: 0.8684 (pp20) cc_final: 0.8479 (pm20) REVERT: G 158 PHE cc_start: 0.8513 (m-80) cc_final: 0.8233 (m-10) REVERT: Z 378 MET cc_start: 0.0621 (mtt) cc_final: 0.0334 (mmm) REVERT: Z 508 MET cc_start: 0.5780 (tpt) cc_final: 0.5530 (tpt) REVERT: Z 740 CYS cc_start: 0.8966 (p) cc_final: 0.8700 (p) outliers start: 90 outliers final: 47 residues processed: 354 average time/residue: 0.2327 time to fit residues: 142.8642 Evaluate side-chains 321 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 683 GLN Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 331 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 395 optimal weight: 0.3980 chunk 457 optimal weight: 20.0000 chunk 401 optimal weight: 0.0570 chunk 424 optimal weight: 3.9990 chunk 486 optimal weight: 9.9990 chunk 271 optimal weight: 3.9990 chunk 466 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 overall best weight: 1.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.077008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.047356 restraints weight = 208787.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.048464 restraints weight = 105947.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049175 restraints weight = 70301.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.049470 restraints weight = 54828.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.049619 restraints weight = 48490.172| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 42424 Z= 0.144 Angle : 0.652 18.993 57648 Z= 0.332 Chirality : 0.046 0.334 6435 Planarity : 0.004 0.105 7144 Dihedral : 14.334 175.434 6402 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 1.49 % Allowed : 13.67 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.12), residues: 4882 helix: 1.00 (0.14), residues: 1535 sheet: -0.73 (0.19), residues: 738 loop : -0.71 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1050 TYR 0.018 0.001 TYR A 827 PHE 0.018 0.001 PHE A 113 TRP 0.014 0.001 TRP B 22 HIS 0.005 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (42412) covalent geometry : angle 0.65153 / 0.33 (57648) hydrogen bonds : bond 0.03730 / 2.55 ( 1625) hydrogen bonds : angle 5.09036 / 3.63 ( 4483) metal coordination : bond 0.00142 / 0.08 ( 8) Misc. bond : bond 0.00808 / 0.39 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 1.710 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 322 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9033 (mm) REVERT: A 417 LYS cc_start: 0.9369 (tttt) cc_final: 0.8972 (tttm) REVERT: A 561 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.8894 (mtp) REVERT: A 1038 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8899 (p) REVERT: A 1086 MET cc_start: 0.9199 (mmm) cc_final: 0.8967 (mmm) REVERT: A 1228 MET cc_start: 0.8554 (mmm) cc_final: 0.8038 (mtt) REVERT: A 1459 MET cc_start: 0.9079 (mtt) cc_final: 0.8828 (mtt) REVERT: M 30 MET cc_start: 0.3706 (ptp) cc_final: 0.3068 (ptp) REVERT: M 276 MET cc_start: 0.4399 (ttp) cc_final: 0.4133 (ttm) REVERT: M 437 MET cc_start: -0.0387 (mmm) cc_final: -0.1119 (mtt) REVERT: M 482 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8845 (pp) REVERT: B 239 MET cc_start: 0.9046 (tpp) cc_final: 0.8667 (tpt) REVERT: B 485 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9241 (mt) REVERT: B 508 MET cc_start: 0.8663 (mmm) cc_final: 0.8182 (mmm) REVERT: B 553 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8670 (mm) REVERT: B 677 MET cc_start: 0.8213 (mmm) cc_final: 0.7965 (tpp) REVERT: B 692 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9006 (p) REVERT: B 764 MET cc_start: 0.8459 (mmt) cc_final: 0.8100 (mtt) REVERT: B 816 GLU cc_start: 0.8243 (tp30) cc_final: 0.7833 (tp30) REVERT: B 840 MET cc_start: 0.6598 (tpp) cc_final: 0.6331 (tpp) REVERT: C 62 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 127 VAL cc_start: 0.8882 (t) cc_final: 0.8466 (p) REVERT: E 94 MET cc_start: 0.8713 (mmm) cc_final: 0.8507 (tpp) REVERT: F 98 LYS cc_start: 0.9363 (mtmt) cc_final: 0.9145 (mtpp) REVERT: H 13 LYS cc_start: 0.9318 (mmtt) cc_final: 0.8793 (mmtm) REVERT: H 92 MET cc_start: 0.8705 (mtp) cc_final: 0.8448 (mtp) REVERT: K 8 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8439 (mm-30) REVERT: K 38 GLU cc_start: 0.8520 (tp30) cc_final: 0.8304 (tp30) REVERT: K 50 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9498 (mt) REVERT: K 102 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8352 (mm-30) REVERT: L 30 SER cc_start: 0.8762 (m) cc_final: 0.8505 (p) REVERT: L 44 MET cc_start: 0.8810 (mmt) cc_final: 0.8482 (mmm) REVERT: G 104 MET cc_start: 0.8242 (tmm) cc_final: 0.7868 (tmm) REVERT: G 158 PHE cc_start: 0.8501 (m-80) cc_final: 0.8233 (m-10) REVERT: Z 378 MET cc_start: 0.0827 (mtt) cc_final: 0.0535 (mmm) REVERT: Z 740 CYS cc_start: 0.8976 (p) cc_final: 0.8704 (p) outliers start: 65 outliers final: 47 residues processed: 328 average time/residue: 0.2378 time to fit residues: 134.7110 Evaluate side-chains 317 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 473 optimal weight: 20.0000 chunk 297 optimal weight: 0.9980 chunk 399 optimal weight: 6.9990 chunk 187 optimal weight: 50.0000 chunk 165 optimal weight: 50.0000 chunk 282 optimal weight: 8.9990 chunk 468 optimal weight: 30.0000 chunk 253 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 298 optimal weight: 0.0570 chunk 237 optimal weight: 0.6980 overall best weight: 3.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN B1094 GLN ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.076180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047488 restraints weight = 210621.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.048659 restraints weight = 111361.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.048394 restraints weight = 70052.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048888 restraints weight = 58722.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.048904 restraints weight = 51590.703| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 42424 Z= 0.187 Angle : 0.669 20.961 57648 Z= 0.341 Chirality : 0.046 0.320 6435 Planarity : 0.004 0.103 7144 Dihedral : 14.306 175.708 6402 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 1.81 % Allowed : 13.83 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.12), residues: 4882 helix: 1.08 (0.14), residues: 1534 sheet: -0.78 (0.19), residues: 733 loop : -0.70 (0.12), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 641 TYR 0.018 0.001 TYR B 752 PHE 0.025 0.001 PHE G 80 TRP 0.018 0.001 TRP B 22 HIS 0.012 0.001 HIS B 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (42412) covalent geometry : angle 0.66908 / 0.34 (57648) hydrogen bonds : bond 0.03798 / 2.59 ( 1625) hydrogen bonds : angle 5.06983 / 3.61 ( 4483) metal coordination : bond 0.00224 / 0.12 ( 8) Misc. bond : bond 0.00843 / 0.41 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 266 time to evaluate : 1.789 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: A 322 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.9004 (mm) REVERT: A 417 LYS cc_start: 0.9410 (tttt) cc_final: 0.9034 (tttm) REVERT: A 561 MET cc_start: 0.9453 (OUTLIER) cc_final: 0.9081 (mtp) REVERT: A 1038 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8935 (p) REVERT: A 1128 ILE cc_start: 0.9796 (mm) cc_final: 0.9560 (pt) REVERT: A 1228 MET cc_start: 0.8661 (mmm) cc_final: 0.8104 (mtt) REVERT: A 1459 MET cc_start: 0.9173 (mtt) cc_final: 0.8963 (mtt) REVERT: M 30 MET cc_start: 0.3498 (ptp) cc_final: 0.2895 (ptp) REVERT: M 61 MET cc_start: 0.6605 (tpp) cc_final: 0.6357 (tpp) REVERT: M 276 MET cc_start: 0.2178 (ttp) cc_final: 0.1894 (ttm) REVERT: M 437 MET cc_start: 0.0238 (mmm) cc_final: -0.0911 (mtt) REVERT: M 482 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9046 (pp) REVERT: B 239 MET cc_start: 0.9095 (tpp) cc_final: 0.8859 (tpt) REVERT: B 485 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9330 (mt) REVERT: B 508 MET cc_start: 0.8744 (mmm) cc_final: 0.8385 (mmm) REVERT: B 692 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9031 (p) REVERT: B 764 MET cc_start: 0.8536 (mmt) cc_final: 0.8163 (mtt) REVERT: B 816 GLU cc_start: 0.8448 (tp30) cc_final: 0.8023 (tp30) REVERT: B 1049 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.8942 (mp10) REVERT: C 15 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8450 (p) REVERT: C 62 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7728 (tm-30) REVERT: C 127 VAL cc_start: 0.9066 (t) cc_final: 0.8635 (p) REVERT: E 94 MET cc_start: 0.8764 (mmm) cc_final: 0.8492 (tpp) REVERT: F 98 LYS cc_start: 0.9383 (mtmt) cc_final: 0.9169 (mtpp) REVERT: H 13 LYS cc_start: 0.9353 (mmtt) cc_final: 0.8763 (mmtm) REVERT: H 92 MET cc_start: 0.8832 (mtp) cc_final: 0.8563 (mtp) REVERT: I 23 MET cc_start: 0.8808 (ttt) cc_final: 0.8437 (ttp) REVERT: K 8 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8499 (mm-30) REVERT: K 38 GLU cc_start: 0.8598 (tp30) cc_final: 0.8178 (tp30) REVERT: K 50 LEU cc_start: 0.9768 (OUTLIER) cc_final: 0.9548 (mt) REVERT: K 102 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8387 (mm-30) REVERT: L 30 SER cc_start: 0.8824 (m) cc_final: 0.8565 (p) REVERT: L 44 MET cc_start: 0.8913 (mmt) cc_final: 0.8603 (mmm) REVERT: G 104 MET cc_start: 0.8024 (tmm) cc_final: 0.7661 (tmm) REVERT: G 158 PHE cc_start: 0.8496 (m-80) cc_final: 0.8266 (m-10) REVERT: Z 474 MET cc_start: 0.8405 (mtp) cc_final: 0.8148 (mmt) REVERT: Z 740 CYS cc_start: 0.9016 (p) cc_final: 0.8762 (p) outliers start: 79 outliers final: 57 residues processed: 330 average time/residue: 0.2201 time to fit residues: 127.0048 Evaluate side-chains 323 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 257 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 246 THR Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain Z residue 260 MET Chi-restraints excluded: chain Z residue 460 MET Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 507 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 265 optimal weight: 0.4980 chunk 243 optimal weight: 0.0470 chunk 244 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 399 optimal weight: 2.9990 chunk 369 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 487 optimal weight: 9.9990 chunk 427 optimal weight: 0.7980 chunk 434 optimal weight: 5.9990 chunk 314 optimal weight: 7.9990 overall best weight: 1.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.076519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.047504 restraints weight = 210495.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.047667 restraints weight = 105316.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.048301 restraints weight = 68875.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.048618 restraints weight = 53706.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048919 restraints weight = 47239.384| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 42424 Z= 0.138 Angle : 0.654 20.431 57648 Z= 0.332 Chirality : 0.046 0.400 6435 Planarity : 0.004 0.095 7144 Dihedral : 14.260 175.209 6402 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 1.65 % Allowed : 14.01 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.12), residues: 4882 helix: 1.08 (0.14), residues: 1538 sheet: -0.71 (0.19), residues: 752 loop : -0.67 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG B1050 TYR 0.020 0.001 TYR F 56 PHE 0.017 0.001 PHE A 113 TRP 0.014 0.001 TRP B 22 HIS 0.006 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (42412) covalent geometry : angle 0.65379 / 0.33 (57648) hydrogen bonds : bond 0.03628 / 2.47 ( 1625) hydrogen bonds : angle 5.02056 / 3.58 ( 4483) metal coordination : bond 0.00113 / 0.06 ( 8) Misc. bond : bond 0.00620 / 0.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 271 time to evaluate : 1.654 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 322 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8989 (mm) REVERT: A 417 LYS cc_start: 0.9373 (tttt) cc_final: 0.8998 (tttm) REVERT: A 561 MET cc_start: 0.9402 (OUTLIER) cc_final: 0.9029 (mtp) REVERT: A 769 MET cc_start: 0.8865 (tpp) cc_final: 0.8634 (mtt) REVERT: A 1038 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8930 (p) REVERT: A 1228 MET cc_start: 0.8621 (mmm) cc_final: 0.8197 (mtt) REVERT: A 1459 MET cc_start: 0.9174 (mtt) cc_final: 0.8958 (mtt) REVERT: M 30 MET cc_start: 0.3690 (ptp) cc_final: 0.3090 (ptp) REVERT: M 61 MET cc_start: 0.6801 (tpp) cc_final: 0.6588 (tpp) REVERT: M 276 MET cc_start: 0.3525 (ttp) cc_final: 0.3189 (ttm) REVERT: M 437 MET cc_start: -0.0008 (mmm) cc_final: -0.0930 (mtt) REVERT: M 482 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9036 (pp) REVERT: B 485 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9176 (mt) REVERT: B 508 MET cc_start: 0.8734 (mmm) cc_final: 0.8491 (mmm) REVERT: B 692 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9070 (p) REVERT: B 764 MET cc_start: 0.8594 (mmt) cc_final: 0.8196 (mtt) REVERT: B 816 GLU cc_start: 0.8436 (tp30) cc_final: 0.8033 (tp30) REVERT: B 840 MET cc_start: 0.6742 (tpp) cc_final: 0.6454 (tpp) REVERT: B 1049 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8969 (mt0) REVERT: C 15 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8554 (p) REVERT: C 62 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7697 (tm-30) REVERT: E 18 MET cc_start: 0.9170 (mmm) cc_final: 0.8943 (mmm) REVERT: E 94 MET cc_start: 0.8791 (mmm) cc_final: 0.8525 (tpp) REVERT: F 98 LYS cc_start: 0.9386 (mtmt) cc_final: 0.9183 (mtpp) REVERT: H 13 LYS cc_start: 0.9317 (mmtt) cc_final: 0.8792 (mmtm) REVERT: H 92 MET cc_start: 0.8769 (mtp) cc_final: 0.8555 (mtp) REVERT: I 23 MET cc_start: 0.8804 (ttt) cc_final: 0.8439 (ttp) REVERT: K 8 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8494 (mm-30) REVERT: K 38 GLU cc_start: 0.8572 (tp30) cc_final: 0.8357 (tp30) REVERT: K 50 LEU cc_start: 0.9741 (OUTLIER) cc_final: 0.9522 (mt) REVERT: K 102 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8311 (mm-30) REVERT: L 30 SER cc_start: 0.8711 (m) cc_final: 0.8462 (p) REVERT: L 37 ARG cc_start: 0.8511 (ptt-90) cc_final: 0.8248 (ptt-90) REVERT: L 44 MET cc_start: 0.8913 (mmt) cc_final: 0.8611 (mmm) REVERT: G 104 MET cc_start: 0.8070 (tmm) cc_final: 0.7696 (tmm) REVERT: G 118 GLU cc_start: 0.8625 (pm20) cc_final: 0.7777 (pm20) REVERT: G 131 MET cc_start: 0.8797 (pmm) cc_final: 0.8390 (mmm) REVERT: G 158 PHE cc_start: 0.8464 (m-80) cc_final: 0.8201 (m-10) REVERT: Y 63 MET cc_start: 0.4088 (ppp) cc_final: 0.3362 (tmm) REVERT: Z 378 MET cc_start: -0.0318 (mmm) cc_final: -0.0627 (mmt) REVERT: Z 740 CYS cc_start: 0.9026 (p) cc_final: 0.8781 (p) outliers start: 72 outliers final: 50 residues processed: 329 average time/residue: 0.2305 time to fit residues: 133.0694 Evaluate side-chains 312 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain Z residue 260 MET Chi-restraints excluded: chain Z residue 460 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 395 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 441 optimal weight: 10.0000 chunk 352 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 262 optimal weight: 0.9980 chunk 217 optimal weight: 20.0000 chunk 386 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 272 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN B1094 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.076243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045845 restraints weight = 210146.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046900 restraints weight = 106674.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.047537 restraints weight = 70615.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.047864 restraints weight = 56072.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.048007 restraints weight = 49894.473| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 42424 Z= 0.155 Angle : 0.657 17.968 57648 Z= 0.335 Chirality : 0.046 0.295 6435 Planarity : 0.004 0.094 7144 Dihedral : 14.203 175.621 6402 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer: Outliers : 1.42 % Allowed : 14.29 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.12), residues: 4882 helix: 1.11 (0.14), residues: 1535 sheet: -0.73 (0.19), residues: 748 loop : -0.66 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 255 TYR 0.028 0.001 TYR A 859 PHE 0.020 0.001 PHE L 55 TRP 0.015 0.001 TRP B 22 HIS 0.007 0.001 HIS C 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (42412) covalent geometry : angle 0.65738 / 0.34 (57648) hydrogen bonds : bond 0.03644 / 2.48 ( 1625) hydrogen bonds : angle 5.00121 / 3.56 ( 4483) metal coordination : bond 0.00153 / 0.08 ( 8) Misc. bond : bond 0.00486 / 0.24 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 258 time to evaluate : 1.671 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 317 MET cc_start: 0.9053 (tmm) cc_final: 0.8580 (tmm) REVERT: A 322 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9008 (mm) REVERT: A 417 LYS cc_start: 0.9373 (tttt) cc_final: 0.8924 (tttm) REVERT: A 561 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.9064 (mtp) REVERT: A 959 MET cc_start: 0.8975 (tpp) cc_final: 0.8736 (mtt) REVERT: A 1038 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8881 (p) REVERT: A 1228 MET cc_start: 0.8568 (mmm) cc_final: 0.8090 (mtt) REVERT: A 1459 MET cc_start: 0.9138 (mtt) cc_final: 0.8930 (mtt) REVERT: M 30 MET cc_start: 0.3459 (ptp) cc_final: 0.2800 (ptp) REVERT: M 276 MET cc_start: 0.4983 (ttp) cc_final: 0.4681 (ttm) REVERT: M 437 MET cc_start: -0.0467 (mmm) cc_final: -0.1097 (mtt) REVERT: M 482 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9148 (pp) REVERT: B 485 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9180 (mt) REVERT: B 508 MET cc_start: 0.8703 (mmm) cc_final: 0.8495 (mmm) REVERT: B 692 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9101 (p) REVERT: B 764 MET cc_start: 0.8657 (mmt) cc_final: 0.8274 (mtt) REVERT: B 816 GLU cc_start: 0.8471 (tp30) cc_final: 0.8096 (tp30) REVERT: B 840 MET cc_start: 0.7016 (tpp) cc_final: 0.6621 (tpp) REVERT: C 15 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8680 (p) REVERT: C 62 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7666 (tm-30) REVERT: C 263 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9410 (tp) REVERT: E 18 MET cc_start: 0.9126 (mmm) cc_final: 0.8860 (mmm) REVERT: F 98 LYS cc_start: 0.9396 (mtmt) cc_final: 0.9134 (mtpp) REVERT: H 13 LYS cc_start: 0.9296 (mmtt) cc_final: 0.8841 (mptt) REVERT: H 92 MET cc_start: 0.8754 (mtp) cc_final: 0.8432 (mtp) REVERT: I 23 MET cc_start: 0.8809 (ttt) cc_final: 0.8462 (ttp) REVERT: K 38 GLU cc_start: 0.8544 (tp30) cc_final: 0.8287 (tp30) REVERT: K 50 LEU cc_start: 0.9759 (OUTLIER) cc_final: 0.9552 (mt) REVERT: K 102 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8282 (mm-30) REVERT: L 25 GLU cc_start: 0.9105 (mp0) cc_final: 0.8836 (mp0) REVERT: L 30 SER cc_start: 0.8794 (m) cc_final: 0.8539 (p) REVERT: L 37 ARG cc_start: 0.8439 (ptt-90) cc_final: 0.8173 (ptt-90) REVERT: L 44 MET cc_start: 0.8936 (mmt) cc_final: 0.8626 (mmm) REVERT: G 104 MET cc_start: 0.8081 (tmm) cc_final: 0.7711 (tmm) REVERT: G 118 GLU cc_start: 0.8616 (pm20) cc_final: 0.8240 (pm20) REVERT: G 158 PHE cc_start: 0.8470 (m-80) cc_final: 0.8214 (m-10) REVERT: Y 63 MET cc_start: -0.0573 (ppp) cc_final: -0.2127 (ttt) REVERT: Z 197 MET cc_start: 0.6882 (mmt) cc_final: 0.6671 (mmt) REVERT: Z 740 CYS cc_start: 0.8953 (p) cc_final: 0.8722 (p) outliers start: 62 outliers final: 49 residues processed: 307 average time/residue: 0.2390 time to fit residues: 128.2333 Evaluate side-chains 307 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 249 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain Z residue 260 MET Chi-restraints excluded: chain Z residue 460 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 273 optimal weight: 0.9990 chunk 457 optimal weight: 40.0000 chunk 275 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 168 optimal weight: 40.0000 chunk 92 optimal weight: 0.3980 chunk 229 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 336 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A1082 HIS ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 631 GLN B 741 HIS ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.076945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.046925 restraints weight = 210758.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.047861 restraints weight = 106847.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.048265 restraints weight = 69806.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.048562 restraints weight = 55771.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.048715 restraints weight = 49877.254| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 42424 Z= 0.123 Angle : 0.658 16.721 57648 Z= 0.333 Chirality : 0.046 0.287 6435 Planarity : 0.004 0.091 7144 Dihedral : 14.170 176.026 6402 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 1.42 % Allowed : 14.65 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.12), residues: 4882 helix: 1.08 (0.14), residues: 1542 sheet: -0.67 (0.19), residues: 761 loop : -0.65 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 31 TYR 0.017 0.001 TYR A 827 PHE 0.022 0.001 PHE L 55 TRP 0.013 0.001 TRP B 236 HIS 0.007 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (42412) covalent geometry : angle 0.65799 / 0.33 (57648) hydrogen bonds : bond 0.03553 / 2.42 ( 1625) hydrogen bonds : angle 4.95643 / 3.53 ( 4483) metal coordination : bond 0.00066 / 0.04 ( 8) Misc. bond : bond 0.00513 / 0.25 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9689.65 seconds wall clock time: 167 minutes 47.90 seconds (10067.90 seconds total)