Starting phenix.real_space_refine on Tue Aug 26 21:19:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4c_17405/08_2025/8p4c_17405.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4c_17405/08_2025/8p4c_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p4c_17405/08_2025/8p4c_17405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4c_17405/08_2025/8p4c_17405.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p4c_17405/08_2025/8p4c_17405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4c_17405/08_2025/8p4c_17405.map" } 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-2.0-5787/lib/python3.9/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: {'RNA': 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: 10.23, per 1000 atoms: 0.25 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: 4.10 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 6.13 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: 14.30 Time building geometry restraints manager: 5.24 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: 57106 3.37 - 6.73: 486 6.73 - 10.10: 46 10.10 - 13.46: 8 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 - 35.48: 25007 35.48 - 70.96: 717 70.96 - 106.44: 42 106.44 - 141.93: 2 141.93 - 177.41: 4 Dihedral angle restraints: 25772 sinusoidal: 11391 harmonic: 14381 Sorted by residual: dihedral pdb=" C5' G P 32 " pdb=" C4' G P 32 " pdb=" C3' G P 32 " pdb=" O3' G P 32 " ideal model delta sinusoidal sigma weight residual 82.00 152.92 -70.92 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" O4' G P 32 " pdb=" C4' G P 32 " pdb=" C3' G P 32 " pdb=" C2' G P 32 " ideal model delta sinusoidal sigma weight residual -35.00 31.43 -66.43 1 8.00e+00 1.56e-02 9.00e+01 dihedral pdb=" C3' G P 32 " pdb=" C4' G P 32 " pdb=" O4' G P 32 " pdb=" C1' G P 32 " ideal model delta sinusoidal sigma weight residual 20.00 -36.37 56.37 1 8.00e+00 1.56e-02 6.69e+01 ... (remaining 25769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 6316 0.134 - 0.268: 107 0.268 - 0.401: 6 0.401 - 0.535: 2 0.535 - 0.669: 4 Chirality restraints: 6435 Sorted by residual: chirality pdb=" C3' G P 36 " pdb=" C4' G P 36 " pdb=" O3' G P 36 " pdb=" C2' G P 36 " both_signs ideal model delta sigma weight residual False -2.74 -2.08 -0.67 2.00e-01 2.50e+01 1.12e+01 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 ... (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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 54.610 Find NCS groups from input model: 0.250 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 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= 0.655 Angle : 0.844 16.828 57648 Z= 0.504 Chirality : 0.055 0.669 6435 Planarity : 0.006 0.134 7144 Dihedral : 15.209 177.407 16468 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 aren 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 covalent geometry : bond 0.00529 (42412) covalent geometry : angle 0.84354 (57648) hydrogen bonds : bond 0.17800 ( 1625) hydrogen bonds : angle 7.29455 ( 4483) metal coordination : bond 0.13650 ( 8) Misc. bond : bond 0.60099 ( 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 : 1.706 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: 0.7323 (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: 0.2556 time to fit residues: 270.8568 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 : 1.766 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 432 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B 980 HIS B1049 GLN C 51 GLN C 260 GLN C 265 HIS 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 616 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.080458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.051755 restraints weight = 212435.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.052762 restraints weight = 108315.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.053408 restraints weight = 70165.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.053959 restraints weight = 54330.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.054074 restraints weight = 46027.239| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 42424 Z= 0.223 Angle : 0.765 20.182 57648 Z= 0.403 Chirality : 0.049 0.333 6435 Planarity : 0.006 0.160 7144 Dihedral : 15.365 179.368 6467 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.20 % Favored : 94.67 % Rotamer: Outliers : 1.30 % Allowed : 9.13 % Favored : 89.56 % 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 aren not related in a simple way. whole: -0.79 (0.12), residues: 4882 helix: 0.41 (0.13), residues: 1523 sheet: -0.71 (0.19), residues: 686 loop : -1.00 (0.12), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Z 555 TYR 0.036 0.002 TYR Z 203 PHE 0.075 0.002 PHE Z 623 TRP 0.024 0.002 TRP M 293 HIS 0.015 0.001 HIS Z 509 Details of bonding type rmsd covalent geometry : bond 0.00479 (42412) covalent geometry : angle 0.76477 (57648) hydrogen bonds : bond 0.04662 ( 1625) hydrogen bonds : angle 5.71013 ( 4483) metal coordination : bond 0.00232 ( 8) Misc. bond : bond 0.00613 ( 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 429 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 372 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 MET cc_start: 0.9313 (mmm) cc_final: 0.9021 (tpp) REVERT: A 561 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8925 (mmm) REVERT: A 861 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8822 (mp10) REVERT: A 1086 MET cc_start: 0.8972 (mmm) cc_final: 0.8670 (mmm) REVERT: A 1108 HIS cc_start: 0.6669 (m-70) cc_final: 0.6388 (m90) REVERT: A 1228 MET cc_start: 0.8468 (mmm) cc_final: 0.7900 (mtt) REVERT: A 1427 LEU cc_start: 0.9424 (mt) cc_final: 0.9090 (tp) REVERT: A 1428 MET cc_start: 0.8600 (tmm) cc_final: 0.8381 (tpp) REVERT: A 1459 MET cc_start: 0.8875 (mtt) cc_final: 0.8366 (mtt) REVERT: M 61 MET cc_start: 0.6209 (tpp) cc_final: 0.5837 (tpp) REVERT: M 396 MET cc_start: 0.6426 (mtt) cc_final: 0.6163 (mtt) REVERT: B 53 MET cc_start: 0.8801 (mpp) cc_final: 0.8346 (mpp) REVERT: B 394 ASP cc_start: 0.8255 (m-30) cc_final: 0.7927 (m-30) REVERT: B 407 MET cc_start: 0.8513 (ptp) cc_final: 0.8294 (ptm) REVERT: B 816 GLU cc_start: 0.7690 (tp30) cc_final: 0.7254 (tp30) REVERT: B 840 MET cc_start: 0.6114 (tpp) cc_final: 0.5442 (tpp) REVERT: B 1172 MET cc_start: 0.8212 (mpp) cc_final: 0.7745 (mpp) REVERT: H 13 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8821 (mmtm) REVERT: K 38 GLU cc_start: 0.8520 (tp30) cc_final: 0.7911 (tp30) REVERT: K 42 LEU cc_start: 0.9733 (mt) cc_final: 0.9485 (mt) REVERT: K 50 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9444 (mt) REVERT: K 102 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8282 (mm-30) REVERT: D 19 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.9209 (pm20) REVERT: G 104 MET cc_start: 0.8172 (tmm) cc_final: 0.7205 (tmm) REVERT: G 158 PHE cc_start: 0.8587 (m-80) cc_final: 0.8305 (m-10) REVERT: Z 460 MET cc_start: 0.7525 (mmt) cc_final: 0.7257 (mmp) outliers start: 57 outliers final: 27 residues processed: 410 average time/residue: 0.2433 time to fit residues: 170.9892 Evaluate side-chains 346 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 315 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 463 SER Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 561 PHE 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 923 VAL Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1145 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 H residue 133 HIS 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 19 GLN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 301 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 302 optimal weight: 0.9990 chunk 491 optimal weight: 4.9990 chunk 148 optimal weight: 0.1980 chunk 127 optimal weight: 3.9990 chunk 374 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 298 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS M 102 ASN ** M 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS C 66 HIS ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS G 60 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.080047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.051089 restraints weight = 212149.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052326 restraints weight = 107456.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.052958 restraints weight = 69956.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.053177 restraints weight = 54344.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.053633 restraints weight = 48369.673| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 42424 Z= 0.146 Angle : 0.651 14.201 57648 Z= 0.341 Chirality : 0.045 0.189 6435 Planarity : 0.004 0.133 7144 Dihedral : 15.122 177.225 6463 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 1.69 % Allowed : 10.05 % Favored : 88.26 % 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 aren not related in a simple way. whole: -0.60 (0.12), residues: 4882 helix: 0.61 (0.14), residues: 1543 sheet: -0.64 (0.19), residues: 682 loop : -0.92 (0.12), residues: 2657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 555 TYR 0.025 0.001 TYR Z 203 PHE 0.032 0.002 PHE Z 621 TRP 0.019 0.001 TRP M 293 HIS 0.008 0.001 HIS Z 477 Details of bonding type rmsd covalent geometry : bond 0.00322 (42412) covalent geometry : angle 0.65061 (57648) hydrogen bonds : bond 0.04190 ( 1625) hydrogen bonds : angle 5.38549 ( 4483) metal coordination : bond 0.00223 ( 8) Misc. bond : bond 0.00934 ( 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 418 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 344 time to evaluate : 1.957 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: A 99 PHE cc_start: 0.9007 (m-10) cc_final: 0.8624 (m-10) REVERT: A 329 MET cc_start: 0.8940 (tpp) cc_final: 0.8735 (tpp) REVERT: A 469 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8553 (mtm) REVERT: A 561 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.9038 (mmm) REVERT: A 1086 MET cc_start: 0.8978 (mmm) cc_final: 0.8694 (mmm) REVERT: A 1228 MET cc_start: 0.8381 (mmm) cc_final: 0.7863 (mtt) REVERT: A 1427 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9009 (tp) REVERT: A 1459 MET cc_start: 0.8932 (mtt) cc_final: 0.8431 (mtt) REVERT: M 61 MET cc_start: 0.5827 (tpp) cc_final: 0.5442 (tpp) REVERT: M 437 MET cc_start: -0.0555 (mmm) cc_final: -0.1580 (mtt) REVERT: B 394 ASP cc_start: 0.8341 (m-30) cc_final: 0.8106 (m-30) REVERT: B 407 MET cc_start: 0.8629 (ptp) cc_final: 0.8412 (ptm) REVERT: B 702 MET cc_start: 0.8443 (mmm) cc_final: 0.8186 (mmp) REVERT: B 764 MET cc_start: 0.8082 (mmm) cc_final: 0.7833 (mmt) REVERT: B 816 GLU cc_start: 0.7825 (tp30) cc_final: 0.7328 (tp30) REVERT: B 840 MET cc_start: 0.6248 (tpp) cc_final: 0.5858 (tpp) REVERT: C 62 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7744 (tm-30) REVERT: E 94 MET cc_start: 0.8471 (mmm) cc_final: 0.8254 (tpp) REVERT: F 94 MET cc_start: 0.8039 (tmm) cc_final: 0.7677 (tmm) REVERT: F 98 LYS cc_start: 0.9297 (mtmt) cc_final: 0.8867 (mtmt) REVERT: H 13 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8809 (mmtm) REVERT: I 69 ILE cc_start: 0.9155 (tp) cc_final: 0.8950 (tp) REVERT: I 108 MET cc_start: 0.8321 (mmp) cc_final: 0.7966 (mmp) REVERT: K 38 GLU cc_start: 0.8510 (tp30) cc_final: 0.8110 (tp30) REVERT: K 50 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9456 (mt) REVERT: K 102 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8334 (mm-30) REVERT: L 30 SER cc_start: 0.8699 (m) cc_final: 0.8407 (p) REVERT: L 34 ILE cc_start: 0.8819 (tp) cc_final: 0.8586 (tt) REVERT: G 16 ARG cc_start: 0.8913 (ptm-80) cc_final: 0.8264 (ptm-80) REVERT: G 35 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8137 (mm-30) REVERT: G 104 MET cc_start: 0.8292 (tmm) cc_final: 0.7964 (tmm) REVERT: G 158 PHE cc_start: 0.8536 (m-80) cc_final: 0.8224 (m-10) REVERT: Z 378 MET cc_start: 0.0615 (mtt) cc_final: 0.0320 (mmm) REVERT: Z 451 MET cc_start: 0.8176 (mmm) cc_final: 0.7945 (mmm) REVERT: Z 460 MET cc_start: 0.7595 (mmt) cc_final: 0.7310 (mmp) REVERT: Z 740 CYS cc_start: 0.8726 (p) cc_final: 0.8460 (p) outliers start: 74 outliers final: 33 residues processed: 400 average time/residue: 0.2554 time to fit residues: 172.0243 Evaluate side-chains 339 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 469 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 1095 LEU Chi-restraints excluded: chain A residue 1427 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 149 ILE 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 746 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain F residue 54 THR 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 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 Chi-restraints excluded: chain Z residue 508 MET Chi-restraints excluded: chain Z residue 623 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 200 optimal weight: 9.9990 chunk 338 optimal weight: 9.9990 chunk 426 optimal weight: 10.0000 chunk 337 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 370 optimal weight: 8.9990 chunk 297 optimal weight: 6.9990 chunk 373 optimal weight: 6.9990 chunk 289 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN A 884 ASN M 90 GLN ** M 537 ASN ** 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 518 HIS B1049 GLN B1060 HIS B1071 ASN ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.074585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.043934 restraints weight = 210148.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.045006 restraints weight = 108118.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.045595 restraints weight = 72644.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.045999 restraints weight = 57793.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.046233 restraints weight = 50748.429| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.007 0.181 42424 Z= 0.300 Angle : 0.772 15.212 57648 Z= 0.402 Chirality : 0.048 0.328 6435 Planarity : 0.005 0.108 7144 Dihedral : 14.999 175.053 6462 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 2.40 % Allowed : 10.87 % Favored : 86.72 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.57 (0.12), residues: 4882 helix: 0.67 (0.13), residues: 1538 sheet: -0.85 (0.19), residues: 690 loop : -0.83 (0.12), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 151 TYR 0.032 0.002 TYR B 418 PHE 0.030 0.002 PHE G 107 TRP 0.024 0.002 TRP B 22 HIS 0.013 0.002 HIS Z 477 Details of bonding type rmsd covalent geometry : bond 0.00659 (42412) covalent geometry : angle 0.77160 (57648) hydrogen bonds : bond 0.04812 ( 1625) hydrogen bonds : angle 5.38032 ( 4483) metal coordination : bond 0.00505 ( 8) Misc. bond : bond 0.00856 ( 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 396 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 291 time to evaluate : 1.773 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 317 MET cc_start: 0.9177 (ttp) cc_final: 0.8597 (tmm) REVERT: A 344 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8492 (ttmm) REVERT: A 417 LYS cc_start: 0.9475 (tttt) cc_final: 0.9088 (tttp) REVERT: A 469 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8510 (mtp) REVERT: A 561 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.8955 (mtp) REVERT: A 1228 MET cc_start: 0.8636 (mmm) cc_final: 0.8161 (mtt) REVERT: A 1459 MET cc_start: 0.9138 (mtt) cc_final: 0.8927 (mtt) REVERT: M 276 MET cc_start: 0.6134 (ttp) cc_final: 0.5101 (tmm) REVERT: M 437 MET cc_start: -0.0452 (mmm) cc_final: -0.1197 (mtt) REVERT: M 482 LEU cc_start: 0.9459 (mt) cc_final: 0.9135 (pp) REVERT: M 553 VAL cc_start: 0.2816 (OUTLIER) cc_final: 0.2351 (m) REVERT: B 584 MET cc_start: 0.8004 (tpt) cc_final: 0.7771 (tpt) REVERT: B 692 THR cc_start: 0.9568 (OUTLIER) cc_final: 0.9160 (p) REVERT: B 764 MET cc_start: 0.8731 (mmm) cc_final: 0.8290 (mtt) REVERT: B 791 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8389 (mm-30) REVERT: B 796 MET cc_start: 0.8992 (mmm) cc_final: 0.8733 (mtp) REVERT: B 816 GLU cc_start: 0.8487 (tp30) cc_final: 0.8184 (tp30) REVERT: B 1049 GLN cc_start: 0.9450 (OUTLIER) cc_final: 0.8918 (mp10) REVERT: C 15 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8614 (p) REVERT: C 62 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7771 (tm-30) REVERT: C 127 VAL cc_start: 0.9177 (t) cc_final: 0.8752 (p) REVERT: F 98 LYS cc_start: 0.9387 (mtmt) cc_final: 0.9141 (mtpp) REVERT: H 13 LYS cc_start: 0.9364 (mmmt) cc_final: 0.8724 (mmtm) REVERT: I 23 MET cc_start: 0.8751 (ttt) cc_final: 0.8430 (ttp) REVERT: K 8 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8609 (mm-30) REVERT: K 38 GLU cc_start: 0.8727 (tp30) cc_final: 0.8248 (tp30) REVERT: K 50 LEU cc_start: 0.9800 (OUTLIER) cc_final: 0.9575 (mm) REVERT: L 30 SER cc_start: 0.8894 (m) cc_final: 0.8661 (p) REVERT: L 56 ASP cc_start: 0.8371 (t0) cc_final: 0.8006 (t0) REVERT: G 16 ARG cc_start: 0.9031 (ptm-80) cc_final: 0.8745 (ptm-80) REVERT: G 104 MET cc_start: 0.8424 (tmm) cc_final: 0.8075 (tmm) REVERT: G 158 PHE cc_start: 0.8603 (m-80) cc_final: 0.8303 (m-10) REVERT: Z 378 MET cc_start: 0.0925 (mtt) cc_final: 0.0625 (mmm) REVERT: Z 460 MET cc_start: 0.7849 (mmt) cc_final: 0.7515 (mmp) REVERT: Z 740 CYS cc_start: 0.8902 (p) cc_final: 0.8650 (p) outliers start: 105 outliers final: 46 residues processed: 373 average time/residue: 0.2496 time to fit residues: 158.0756 Evaluate side-chains 305 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 469 MET 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 1095 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 612 ILE 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 1049 GLN 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 263 LEU Chi-restraints excluded: chain E residue 58 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 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 D residue 24 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 623 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 226 optimal weight: 10.0000 chunk 177 optimal weight: 50.0000 chunk 151 optimal weight: 7.9990 chunk 341 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 384 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 415 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1313 GLN M 465 ASN M 537 ASN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 91 HIS ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.074206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.044632 restraints weight = 208298.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.044525 restraints weight = 106360.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.045189 restraints weight = 69556.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045403 restraints weight = 54209.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.045677 restraints weight = 48234.654| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 42424 Z= 0.250 Angle : 0.670 15.877 57648 Z= 0.348 Chirality : 0.045 0.226 6435 Planarity : 0.004 0.091 7144 Dihedral : 14.954 175.052 6462 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.84 % Rotamer: Outliers : 2.24 % Allowed : 12.25 % Favored : 85.51 % 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 aren not related in a simple way. whole: -0.44 (0.12), residues: 4882 helix: 0.87 (0.14), residues: 1540 sheet: -0.87 (0.19), residues: 710 loop : -0.79 (0.12), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 31 TYR 0.022 0.002 TYR F 56 PHE 0.021 0.002 PHE Z 621 TRP 0.017 0.002 TRP B 99 HIS 0.006 0.001 HIS Z 509 Details of bonding type rmsd covalent geometry : bond 0.00549 (42412) covalent geometry : angle 0.66954 (57648) hydrogen bonds : bond 0.04030 ( 1625) hydrogen bonds : angle 5.21365 ( 4483) metal coordination : bond 0.00329 ( 8) Misc. bond : bond 0.00422 ( 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 362 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 264 time to evaluate : 1.707 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 317 MET cc_start: 0.9153 (ttp) cc_final: 0.8764 (tmm) REVERT: A 355 MET cc_start: 0.9172 (mmp) cc_final: 0.8968 (mmp) REVERT: A 469 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8563 (mtp) REVERT: A 561 MET cc_start: 0.9462 (OUTLIER) cc_final: 0.8994 (mtp) REVERT: A 849 ASP cc_start: 0.8966 (m-30) cc_final: 0.8755 (m-30) REVERT: A 890 ARG cc_start: 0.9385 (OUTLIER) cc_final: 0.9008 (mmt180) REVERT: A 1228 MET cc_start: 0.8577 (mmm) cc_final: 0.8332 (mtt) REVERT: M 61 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.5934 (tpp) REVERT: M 276 MET cc_start: 0.3906 (ttp) cc_final: 0.2856 (tmm) REVERT: M 437 MET cc_start: 0.0574 (mmm) cc_final: -0.0495 (mtt) REVERT: M 482 LEU cc_start: 0.9488 (mt) cc_final: 0.9185 (pp) REVERT: M 553 VAL cc_start: 0.3345 (OUTLIER) cc_final: 0.3024 (m) REVERT: M 557 MET cc_start: 0.3238 (ttt) cc_final: 0.3022 (tmm) REVERT: B 347 MET cc_start: 0.8927 (tmm) cc_final: 0.8701 (tmm) REVERT: B 677 MET cc_start: 0.8662 (tpp) cc_final: 0.8225 (tpp) REVERT: B 764 MET cc_start: 0.8641 (mmm) cc_final: 0.8416 (mtt) REVERT: B 863 ASP cc_start: 0.7144 (t0) cc_final: 0.6760 (t0) REVERT: B 1054 MET cc_start: 0.9065 (mpp) cc_final: 0.8481 (mpp) REVERT: B 1081 ASP cc_start: 0.8950 (t0) cc_final: 0.8706 (t0) REVERT: C 15 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8842 (p) REVERT: E 199 THR cc_start: 0.9643 (OUTLIER) cc_final: 0.9383 (t) REVERT: F 98 LYS cc_start: 0.9394 (mtmt) cc_final: 0.9145 (mtmm) REVERT: H 13 LYS cc_start: 0.9401 (mmmt) cc_final: 0.8731 (mmtm) REVERT: I 23 MET cc_start: 0.8776 (ttt) cc_final: 0.8469 (ttp) REVERT: K 8 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8551 (mm-30) REVERT: K 38 GLU cc_start: 0.8635 (tp30) cc_final: 0.8209 (tp30) REVERT: K 50 LEU cc_start: 0.9817 (OUTLIER) cc_final: 0.9607 (mm) REVERT: K 102 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8333 (mm-30) REVERT: L 30 SER cc_start: 0.8949 (m) cc_final: 0.8690 (p) REVERT: G 16 ARG cc_start: 0.9048 (ptm-80) cc_final: 0.8610 (ptm-80) REVERT: G 104 MET cc_start: 0.8387 (tmm) cc_final: 0.8060 (tmm) REVERT: G 158 PHE cc_start: 0.8587 (m-80) cc_final: 0.8380 (m-10) REVERT: Z 378 MET cc_start: -0.0605 (mtt) cc_final: -0.0827 (mmm) REVERT: Z 451 MET cc_start: 0.8112 (mmm) cc_final: 0.7814 (mmm) REVERT: Z 460 MET cc_start: 0.7757 (mmt) cc_final: 0.7532 (mmt) REVERT: Z 474 MET cc_start: 0.7498 (mtt) cc_final: 0.6854 (mmm) REVERT: Z 740 CYS cc_start: 0.8859 (p) cc_final: 0.8604 (p) outliers start: 98 outliers final: 47 residues processed: 345 average time/residue: 0.2463 time to fit residues: 145.6258 Evaluate side-chains 305 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 469 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 565 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 890 ARG 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 61 MET Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 246 THR Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain E residue 58 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 105 ILE Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 101 LEU 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 13 LEU Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 214 optimal weight: 0.8980 chunk 483 optimal weight: 50.0000 chunk 99 optimal weight: 0.8980 chunk 426 optimal weight: 7.9990 chunk 143 optimal weight: 40.0000 chunk 174 optimal weight: 0.1980 chunk 210 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 423 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 537 ASN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 HIS B1049 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN I 91 HIS ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.075441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.045778 restraints weight = 209295.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.045976 restraints weight = 105374.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046585 restraints weight = 69369.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.047060 restraints weight = 54293.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.047139 restraints weight = 47313.810| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42424 Z= 0.130 Angle : 0.629 13.215 57648 Z= 0.324 Chirality : 0.044 0.294 6435 Planarity : 0.004 0.086 7144 Dihedral : 14.876 175.158 6462 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 1.76 % Allowed : 13.46 % Favored : 84.78 % 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 aren not related in a simple way. whole: -0.30 (0.12), residues: 4882 helix: 1.00 (0.14), residues: 1540 sheet: -0.81 (0.19), residues: 719 loop : -0.70 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 16 TYR 0.021 0.001 TYR A 827 PHE 0.018 0.001 PHE Z 621 TRP 0.016 0.001 TRP B 506 HIS 0.010 0.001 HIS B 577 Details of bonding type rmsd covalent geometry : bond 0.00290 (42412) covalent geometry : angle 0.62900 (57648) hydrogen bonds : bond 0.03738 ( 1625) hydrogen bonds : angle 5.02640 ( 4483) metal coordination : bond 0.00082 ( 8) Misc. bond : bond 0.00370 ( 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 352 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 275 time to evaluate : 1.777 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 317 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8780 (tmm) REVERT: A 322 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8966 (mm) REVERT: A 447 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8279 (mt-10) REVERT: A 469 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8622 (mtp) REVERT: A 561 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.9037 (mtp) REVERT: A 849 ASP cc_start: 0.8920 (m-30) cc_final: 0.8654 (m-30) REVERT: A 1228 MET cc_start: 0.8589 (mmm) cc_final: 0.8155 (mtt) REVERT: M 61 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6199 (tpp) REVERT: M 276 MET cc_start: 0.5074 (ttp) cc_final: 0.4044 (tmm) REVERT: M 437 MET cc_start: -0.0075 (mmm) cc_final: -0.0880 (mtt) REVERT: M 482 LEU cc_start: 0.9470 (mt) cc_final: 0.9206 (pp) REVERT: M 553 VAL cc_start: 0.3049 (OUTLIER) cc_final: 0.2763 (m) REVERT: B 347 MET cc_start: 0.8936 (tmm) cc_final: 0.8686 (tmm) REVERT: B 677 MET cc_start: 0.8686 (tpp) cc_final: 0.8305 (tpp) REVERT: B 692 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9195 (p) REVERT: B 764 MET cc_start: 0.8627 (mmm) cc_final: 0.8345 (mtt) REVERT: B 863 ASP cc_start: 0.7096 (t0) cc_final: 0.6662 (t0) REVERT: B 1075 MET cc_start: 0.8956 (tpp) cc_final: 0.8611 (tpp) REVERT: B 1081 ASP cc_start: 0.8999 (t0) cc_final: 0.8720 (t0) REVERT: C 15 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8870 (p) REVERT: E 199 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9372 (t) REVERT: F 98 LYS cc_start: 0.9448 (mtmt) cc_final: 0.9211 (mtpp) REVERT: H 13 LYS cc_start: 0.9370 (mmmt) cc_final: 0.8707 (mmtm) REVERT: I 23 MET cc_start: 0.8804 (ttt) cc_final: 0.8535 (ttp) REVERT: K 8 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8524 (mm-30) REVERT: K 38 GLU cc_start: 0.8537 (tp30) cc_final: 0.8150 (tp30) REVERT: K 102 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8274 (mm-30) REVERT: L 30 SER cc_start: 0.8854 (m) cc_final: 0.8614 (p) REVERT: L 56 ASP cc_start: 0.8118 (t0) cc_final: 0.7792 (t0) REVERT: G 16 ARG cc_start: 0.8995 (ptm-80) cc_final: 0.8490 (ptm-80) REVERT: G 35 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8278 (mm-30) REVERT: G 104 MET cc_start: 0.8491 (tmm) cc_final: 0.8159 (tmm) REVERT: G 158 PHE cc_start: 0.8557 (m-80) cc_final: 0.8257 (m-10) REVERT: Z 378 MET cc_start: 0.0611 (mtt) cc_final: 0.0332 (mmm) REVERT: Z 451 MET cc_start: 0.8178 (mmm) cc_final: 0.7911 (mmm) REVERT: Z 460 MET cc_start: 0.7733 (mmt) cc_final: 0.7455 (mmt) REVERT: Z 474 MET cc_start: 0.7403 (mtt) cc_final: 0.6703 (mmm) REVERT: Z 740 CYS cc_start: 0.8786 (p) cc_final: 0.8563 (p) outliers start: 77 outliers final: 43 residues processed: 334 average time/residue: 0.2493 time to fit residues: 142.0772 Evaluate side-chains 312 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 317 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 469 MET 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 1095 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 612 ILE 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 809 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU 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 H residue 25 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain K residue 13 PHE 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 105 SER Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 493 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 331 optimal weight: 0.0010 chunk 89 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 395 optimal weight: 0.6980 chunk 457 optimal weight: 50.0000 chunk 401 optimal weight: 0.9980 chunk 424 optimal weight: 0.9990 chunk 486 optimal weight: 30.0000 chunk 271 optimal weight: 3.9990 chunk 466 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN A 606 HIS ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS D 55 GLN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.076008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046191 restraints weight = 208005.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.046770 restraints weight = 105561.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.047425 restraints weight = 69263.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.047754 restraints weight = 54600.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047913 restraints weight = 48147.175| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 42424 Z= 0.122 Angle : 0.626 14.596 57648 Z= 0.322 Chirality : 0.044 0.217 6435 Planarity : 0.004 0.085 7144 Dihedral : 14.762 175.387 6462 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 1.60 % Allowed : 13.80 % Favored : 84.59 % 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 aren not related in a simple way. whole: -0.20 (0.12), residues: 4882 helix: 1.10 (0.14), residues: 1538 sheet: -0.68 (0.19), residues: 727 loop : -0.68 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 528 TYR 0.018 0.001 TYR A 827 PHE 0.041 0.001 PHE G 107 TRP 0.018 0.001 TRP C 49 HIS 0.006 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00270 (42412) covalent geometry : angle 0.62650 (57648) hydrogen bonds : bond 0.03574 ( 1625) hydrogen bonds : angle 4.92043 ( 4483) metal coordination : bond 0.00080 ( 8) Misc. bond : bond 0.00437 ( 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 350 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 280 time to evaluate : 1.734 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 317 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8845 (tmm) REVERT: A 322 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8951 (mm) REVERT: A 329 MET cc_start: 0.9291 (tpp) cc_final: 0.8849 (tpp) REVERT: A 417 LYS cc_start: 0.9442 (tttt) cc_final: 0.8981 (tttm) REVERT: A 447 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8302 (mt-10) REVERT: A 469 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8564 (mtp) REVERT: A 561 MET cc_start: 0.9456 (OUTLIER) cc_final: 0.9026 (mtp) REVERT: A 769 MET cc_start: 0.8872 (tpp) cc_final: 0.8509 (mtt) REVERT: A 849 ASP cc_start: 0.8950 (m-30) cc_final: 0.8696 (m-30) REVERT: A 890 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.9028 (mmt180) REVERT: A 1228 MET cc_start: 0.8553 (mmm) cc_final: 0.8347 (mtt) REVERT: M 61 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.6055 (tpp) REVERT: M 276 MET cc_start: 0.5080 (ttp) cc_final: 0.3274 (tmm) REVERT: M 437 MET cc_start: -0.0408 (mmm) cc_final: -0.1151 (mtt) REVERT: M 482 LEU cc_start: 0.9450 (mt) cc_final: 0.9160 (pp) REVERT: M 553 VAL cc_start: 0.2684 (OUTLIER) cc_final: 0.2050 (m) REVERT: M 558 LEU cc_start: 0.5182 (OUTLIER) cc_final: 0.4890 (pp) REVERT: B 108 MET cc_start: 0.8230 (ttm) cc_final: 0.7896 (ttp) REVERT: B 239 MET cc_start: 0.9026 (tpt) cc_final: 0.8637 (tpt) REVERT: B 347 MET cc_start: 0.8945 (tmm) cc_final: 0.8677 (tmm) REVERT: B 485 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9263 (mt) REVERT: B 692 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9189 (p) REVERT: B 764 MET cc_start: 0.8660 (mmm) cc_final: 0.8317 (mtt) REVERT: B 796 MET cc_start: 0.8873 (mmm) cc_final: 0.8519 (mtp) REVERT: B 863 ASP cc_start: 0.7038 (t0) cc_final: 0.6615 (t0) REVERT: B 908 MET cc_start: 0.8605 (tmm) cc_final: 0.8281 (tmm) REVERT: B 1075 MET cc_start: 0.8936 (tpp) cc_final: 0.8635 (tpp) REVERT: B 1081 ASP cc_start: 0.9035 (t0) cc_final: 0.8720 (t0) REVERT: B 1089 MET cc_start: 0.7944 (mtt) cc_final: 0.7681 (mtm) REVERT: C 15 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8899 (p) REVERT: F 98 LYS cc_start: 0.9455 (mtmt) cc_final: 0.9240 (mtpp) REVERT: H 13 LYS cc_start: 0.9370 (mmmt) cc_final: 0.8722 (mmtm) REVERT: I 23 MET cc_start: 0.8816 (ttt) cc_final: 0.8577 (ttp) REVERT: J 41 LYS cc_start: 0.9301 (tppt) cc_final: 0.9034 (mmmt) REVERT: K 8 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8552 (mm-30) REVERT: K 38 GLU cc_start: 0.8496 (tp30) cc_final: 0.8082 (tp30) REVERT: K 102 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8284 (mm-30) REVERT: L 30 SER cc_start: 0.8804 (m) cc_final: 0.8568 (p) REVERT: G 16 ARG cc_start: 0.8981 (ptm-80) cc_final: 0.8546 (ptm-80) REVERT: G 35 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8194 (mm-30) REVERT: G 104 MET cc_start: 0.8479 (tmm) cc_final: 0.8124 (tmm) REVERT: G 158 PHE cc_start: 0.8515 (m-80) cc_final: 0.8229 (m-10) REVERT: Z 378 MET cc_start: 0.0633 (mtt) cc_final: 0.0368 (mmm) REVERT: Z 451 MET cc_start: 0.8140 (mmm) cc_final: 0.7907 (mmm) REVERT: Z 460 MET cc_start: 0.7781 (mmt) cc_final: 0.7492 (mmt) REVERT: Z 474 MET cc_start: 0.7300 (mtt) cc_final: 0.6644 (tpp) REVERT: Z 740 CYS cc_start: 0.8786 (p) cc_final: 0.8565 (p) outliers start: 70 outliers final: 38 residues processed: 335 average time/residue: 0.2472 time to fit residues: 141.4767 Evaluate side-chains 310 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 261 time to evaluate : 1.718 ------------------------------------------------------------------------------- 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 317 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 469 MET 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 890 ARG Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 612 ILE 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 759 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR 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 F residue 90 LEU Chi-restraints excluded: chain H residue 59 VAL 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 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 Z residue 493 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 473 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 399 optimal weight: 3.9990 chunk 187 optimal weight: 30.0000 chunk 165 optimal weight: 0.8980 chunk 282 optimal weight: 10.0000 chunk 468 optimal weight: 50.0000 chunk 253 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 HIS ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 642 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 = 0.3656 r_free = 0.3656 target = 0.074569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.044894 restraints weight = 208273.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.045024 restraints weight = 106156.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.045599 restraints weight = 69792.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.045805 restraints weight = 54965.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.046099 restraints weight = 49230.669| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 42424 Z= 0.190 Angle : 0.645 13.061 57648 Z= 0.333 Chirality : 0.044 0.285 6435 Planarity : 0.004 0.087 7144 Dihedral : 14.644 176.951 6462 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.18 % Favored : 94.76 % Rotamer: Outliers : 1.58 % Allowed : 14.26 % Favored : 84.16 % 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 aren not related in a simple way. whole: -0.19 (0.12), residues: 4882 helix: 1.14 (0.14), residues: 1541 sheet: -0.70 (0.19), residues: 745 loop : -0.69 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 58 TYR 0.022 0.001 TYR A 827 PHE 0.030 0.001 PHE G 107 TRP 0.014 0.001 TRP C 49 HIS 0.018 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00422 (42412) covalent geometry : angle 0.64548 (57648) hydrogen bonds : bond 0.03751 ( 1625) hydrogen bonds : angle 4.93265 ( 4483) metal coordination : bond 0.00345 ( 8) Misc. bond : bond 0.00382 ( 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 330 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 261 time to evaluate : 1.727 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: A 317 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8821 (tmm) REVERT: A 322 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9021 (mm) REVERT: A 329 MET cc_start: 0.9358 (tpp) cc_final: 0.9036 (mmm) REVERT: A 405 LEU cc_start: 0.9733 (OUTLIER) cc_final: 0.9451 (tp) REVERT: A 417 LYS cc_start: 0.9456 (tttt) cc_final: 0.8976 (tttm) REVERT: A 469 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8607 (mtp) REVERT: A 561 MET cc_start: 0.9471 (OUTLIER) cc_final: 0.9115 (mtp) REVERT: A 769 MET cc_start: 0.8915 (tpp) cc_final: 0.8550 (mtt) REVERT: A 849 ASP cc_start: 0.8985 (m-30) cc_final: 0.8734 (m-30) REVERT: A 868 MET cc_start: 0.8855 (mmm) cc_final: 0.8578 (mmm) REVERT: A 890 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8870 (mmt180) REVERT: A 1228 MET cc_start: 0.8610 (mmm) cc_final: 0.8204 (mtt) REVERT: A 1262 MET cc_start: 0.6469 (tpt) cc_final: 0.6159 (tpt) REVERT: M 49 MET cc_start: 0.0963 (ppp) cc_final: 0.0749 (ptt) REVERT: M 61 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.5858 (tpp) REVERT: M 276 MET cc_start: 0.4468 (ttp) cc_final: 0.3228 (tmm) REVERT: M 437 MET cc_start: -0.0102 (mmm) cc_final: -0.1019 (mtt) REVERT: M 482 LEU cc_start: 0.9526 (mt) cc_final: 0.9252 (pp) REVERT: M 553 VAL cc_start: 0.2957 (OUTLIER) cc_final: 0.2537 (m) REVERT: B 239 MET cc_start: 0.9005 (tpt) cc_final: 0.8643 (tpt) REVERT: B 347 MET cc_start: 0.8905 (tmm) cc_final: 0.8687 (tmm) REVERT: B 388 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.8382 (t80) REVERT: B 485 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9259 (mt) REVERT: B 692 THR cc_start: 0.9572 (OUTLIER) cc_final: 0.9229 (p) REVERT: B 764 MET cc_start: 0.8699 (mmm) cc_final: 0.8414 (mtt) REVERT: B 863 ASP cc_start: 0.7361 (t0) cc_final: 0.6920 (t0) REVERT: B 908 MET cc_start: 0.8745 (tmm) cc_final: 0.8435 (tmm) REVERT: B 1075 MET cc_start: 0.9004 (tpp) cc_final: 0.8799 (mmm) REVERT: B 1081 ASP cc_start: 0.9123 (t0) cc_final: 0.8791 (t0) REVERT: C 15 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8884 (p) REVERT: C 62 GLU cc_start: 0.8249 (tm-30) cc_final: 0.8033 (tp30) REVERT: E 121 MET cc_start: 0.8517 (pmm) cc_final: 0.8180 (pmm) REVERT: F 98 LYS cc_start: 0.9481 (mtmt) cc_final: 0.9277 (mtpp) REVERT: H 13 LYS cc_start: 0.9369 (mmmt) cc_final: 0.8860 (mmtm) REVERT: I 23 MET cc_start: 0.8904 (ttt) cc_final: 0.8599 (ttp) REVERT: K 38 GLU cc_start: 0.8505 (tp30) cc_final: 0.8140 (tp30) REVERT: L 30 SER cc_start: 0.8974 (m) cc_final: 0.8721 (p) REVERT: L 44 MET cc_start: 0.9136 (mmt) cc_final: 0.8735 (mmm) REVERT: G 16 ARG cc_start: 0.9023 (ptm-80) cc_final: 0.8543 (ptm-80) REVERT: G 35 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8305 (mm-30) REVERT: G 104 MET cc_start: 0.8558 (tmm) cc_final: 0.8181 (tmm) REVERT: G 158 PHE cc_start: 0.8562 (m-80) cc_final: 0.8341 (m-10) REVERT: Z 378 MET cc_start: 0.0008 (mtt) cc_final: -0.0247 (mmm) REVERT: Z 451 MET cc_start: 0.8155 (mmm) cc_final: 0.7951 (mmm) REVERT: Z 460 MET cc_start: 0.7874 (mmt) cc_final: 0.7587 (mmt) REVERT: Z 474 MET cc_start: 0.7368 (mtt) cc_final: 0.6719 (tpp) outliers start: 69 outliers final: 40 residues processed: 312 average time/residue: 0.2466 time to fit residues: 131.6501 Evaluate side-chains 307 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 255 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 317 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 469 MET 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 890 ARG Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 612 ILE 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 759 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain E residue 36 THR 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 H residue 25 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain K residue 13 PHE 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 Z residue 493 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 265 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 244 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 399 optimal weight: 0.6980 chunk 369 optimal weight: 3.9990 chunk 240 optimal weight: 0.0040 chunk 487 optimal weight: 30.0000 chunk 427 optimal weight: 3.9990 chunk 434 optimal weight: 10.0000 chunk 314 optimal weight: 6.9990 overall best weight: 1.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** Z 642 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 = 0.3672 r_free = 0.3672 target = 0.075291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.045296 restraints weight = 208632.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.046092 restraints weight = 105578.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.046675 restraints weight = 69929.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.047087 restraints weight = 55301.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.047182 restraints weight = 48608.282| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42424 Z= 0.134 Angle : 0.637 13.531 57648 Z= 0.326 Chirality : 0.044 0.266 6435 Planarity : 0.004 0.085 7144 Dihedral : 14.569 176.441 6462 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.92 % Favored : 95.00 % Rotamer: Outliers : 1.49 % Allowed : 14.65 % Favored : 83.86 % 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 aren not related in a simple way. whole: -0.18 (0.12), residues: 4882 helix: 1.11 (0.14), residues: 1546 sheet: -0.67 (0.19), residues: 729 loop : -0.66 (0.12), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 58 TYR 0.018 0.001 TYR A 827 PHE 0.025 0.001 PHE G 107 TRP 0.015 0.001 TRP C 49 HIS 0.017 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00302 (42412) covalent geometry : angle 0.63728 (57648) hydrogen bonds : bond 0.03525 ( 1625) hydrogen bonds : angle 4.86119 ( 4483) metal coordination : bond 0.00110 ( 8) Misc. bond : bond 0.00351 ( 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 328 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 263 time to evaluate : 1.740 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 317 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8824 (tmm) REVERT: A 322 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9015 (mm) REVERT: A 329 MET cc_start: 0.9322 (tpp) cc_final: 0.8977 (mmm) REVERT: A 341 GLN cc_start: 0.9224 (mt0) cc_final: 0.8672 (mt0) REVERT: A 405 LEU cc_start: 0.9735 (OUTLIER) cc_final: 0.9427 (tp) REVERT: A 417 LYS cc_start: 0.9417 (tttt) cc_final: 0.8925 (tttm) REVERT: A 469 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8627 (mtp) REVERT: A 561 MET cc_start: 0.9473 (OUTLIER) cc_final: 0.9093 (mtp) REVERT: A 769 MET cc_start: 0.8912 (tpp) cc_final: 0.8519 (mtt) REVERT: A 849 ASP cc_start: 0.8963 (m-30) cc_final: 0.8711 (m-30) REVERT: A 890 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8853 (mmt180) REVERT: A 1228 MET cc_start: 0.8498 (mmm) cc_final: 0.8212 (mtt) REVERT: M 61 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5956 (tpp) REVERT: M 276 MET cc_start: 0.5575 (ttp) cc_final: 0.4271 (tmm) REVERT: M 437 MET cc_start: -0.0391 (mmm) cc_final: -0.1139 (mtt) REVERT: M 482 LEU cc_start: 0.9517 (mt) cc_final: 0.9230 (pp) REVERT: M 553 VAL cc_start: 0.2777 (OUTLIER) cc_final: 0.2249 (m) REVERT: B 239 MET cc_start: 0.9080 (tpt) cc_final: 0.8733 (tpt) REVERT: B 347 MET cc_start: 0.8891 (tmm) cc_final: 0.8665 (tmm) REVERT: B 388 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8326 (t80) REVERT: B 485 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9239 (mt) REVERT: B 692 THR cc_start: 0.9539 (OUTLIER) cc_final: 0.9202 (p) REVERT: B 764 MET cc_start: 0.8719 (mmm) cc_final: 0.8384 (mtt) REVERT: B 863 ASP cc_start: 0.7380 (t0) cc_final: 0.6912 (t0) REVERT: B 908 MET cc_start: 0.8715 (tmm) cc_final: 0.8409 (tmm) REVERT: B 1081 ASP cc_start: 0.9101 (t0) cc_final: 0.8769 (t0) REVERT: C 15 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8879 (p) REVERT: C 62 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7992 (tp30) REVERT: E 121 MET cc_start: 0.8467 (pmm) cc_final: 0.8149 (pmm) REVERT: F 98 LYS cc_start: 0.9475 (mtmt) cc_final: 0.9274 (mtpp) REVERT: H 13 LYS cc_start: 0.9342 (mmmt) cc_final: 0.8855 (mmtm) REVERT: H 24 ARG cc_start: 0.8912 (ttm110) cc_final: 0.8394 (ttm110) REVERT: I 23 MET cc_start: 0.8890 (ttt) cc_final: 0.8637 (ttp) REVERT: K 38 GLU cc_start: 0.8560 (tp30) cc_final: 0.8153 (tp30) REVERT: K 102 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8357 (mm-30) REVERT: L 30 SER cc_start: 0.8923 (m) cc_final: 0.8682 (p) REVERT: L 44 MET cc_start: 0.9083 (mmt) cc_final: 0.8704 (mmm) REVERT: G 16 ARG cc_start: 0.9002 (ptm-80) cc_final: 0.8522 (ptm-80) REVERT: G 35 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8200 (mm-30) REVERT: G 104 MET cc_start: 0.8568 (tmm) cc_final: 0.8145 (tmm) REVERT: G 158 PHE cc_start: 0.8544 (m-80) cc_final: 0.8319 (m-10) REVERT: Y 63 MET cc_start: -0.0471 (ppp) cc_final: -0.1923 (ttm) REVERT: Z 451 MET cc_start: 0.8128 (mmm) cc_final: 0.7916 (mmm) REVERT: Z 460 MET cc_start: 0.7859 (mmt) cc_final: 0.7554 (mmt) REVERT: Z 474 MET cc_start: 0.7241 (mtt) cc_final: 0.6506 (mmm) outliers start: 65 outliers final: 43 residues processed: 311 average time/residue: 0.2542 time to fit residues: 134.3505 Evaluate side-chains 313 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 317 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 612 ILE 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 759 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR 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 H residue 25 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 101 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 105 SER Chi-restraints excluded: chain Z residue 493 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 395 optimal weight: 0.0270 chunk 255 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 441 optimal weight: 40.0000 chunk 352 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 386 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 272 optimal weight: 3.9990 overall best weight: 3.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.074170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.044712 restraints weight = 207932.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.044667 restraints weight = 106129.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.045283 restraints weight = 69923.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.045615 restraints weight = 55220.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045710 restraints weight = 48484.493| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 42424 Z= 0.195 Angle : 0.673 13.366 57648 Z= 0.344 Chirality : 0.044 0.259 6435 Planarity : 0.004 0.088 7144 Dihedral : 14.525 177.401 6462 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.59 % Rotamer: Outliers : 1.44 % Allowed : 14.70 % Favored : 83.86 % 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 aren not related in a simple way. whole: -0.16 (0.12), residues: 4882 helix: 1.15 (0.14), residues: 1546 sheet: -0.72 (0.19), residues: 746 loop : -0.65 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 58 TYR 0.036 0.001 TYR B1048 PHE 0.023 0.001 PHE G 107 TRP 0.015 0.001 TRP B 22 HIS 0.016 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00434 (42412) covalent geometry : angle 0.67328 (57648) hydrogen bonds : bond 0.03736 ( 1625) hydrogen bonds : angle 4.90960 ( 4483) metal coordination : bond 0.00251 ( 8) Misc. bond : bond 0.00359 ( 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 318 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8872 (tmm) REVERT: A 322 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9034 (mm) REVERT: A 329 MET cc_start: 0.9314 (tpp) cc_final: 0.8994 (mmm) REVERT: A 405 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9387 (tp) REVERT: A 417 LYS cc_start: 0.9437 (tttt) cc_final: 0.8933 (tttm) REVERT: A 469 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8537 (mtp) REVERT: A 561 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.9122 (mtp) REVERT: A 769 MET cc_start: 0.8955 (tpp) cc_final: 0.8649 (mtt) REVERT: A 849 ASP cc_start: 0.8977 (m-30) cc_final: 0.8724 (m-30) REVERT: A 890 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.8898 (mmt180) REVERT: M 61 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.5791 (tpp) REVERT: M 276 MET cc_start: 0.4264 (ttp) cc_final: 0.3049 (tmm) REVERT: M 437 MET cc_start: 0.0228 (mmm) cc_final: -0.0766 (mtt) REVERT: M 482 LEU cc_start: 0.9586 (mt) cc_final: 0.9230 (pp) REVERT: M 553 VAL cc_start: 0.3065 (OUTLIER) cc_final: 0.2578 (m) REVERT: B 239 MET cc_start: 0.9073 (tpt) cc_final: 0.8764 (tpt) REVERT: B 347 MET cc_start: 0.8852 (tmm) cc_final: 0.8616 (tmm) REVERT: B 388 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.8423 (t80) REVERT: B 485 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9263 (mt) REVERT: B 692 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9215 (p) REVERT: B 764 MET cc_start: 0.8768 (mmm) cc_final: 0.8428 (mtt) REVERT: B 863 ASP cc_start: 0.7555 (t0) cc_final: 0.7060 (t0) REVERT: B 908 MET cc_start: 0.8807 (tmm) cc_final: 0.8522 (tmm) REVERT: B 1054 MET cc_start: 0.8988 (mtt) cc_final: 0.8637 (mtt) REVERT: B 1081 ASP cc_start: 0.9162 (t0) cc_final: 0.8828 (t0) REVERT: C 15 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8857 (p) REVERT: F 98 LYS cc_start: 0.9479 (mtmt) cc_final: 0.9279 (mtpp) REVERT: H 13 LYS cc_start: 0.9378 (mmmt) cc_final: 0.9055 (mmmm) REVERT: H 24 ARG cc_start: 0.8933 (ttm110) cc_final: 0.8386 (ttm110) REVERT: H 92 MET cc_start: 0.8808 (mtp) cc_final: 0.8482 (mtp) REVERT: H 145 MET cc_start: 0.8476 (tpp) cc_final: 0.8269 (tpt) REVERT: I 23 MET cc_start: 0.8895 (ttt) cc_final: 0.8648 (ttp) REVERT: K 38 GLU cc_start: 0.8582 (tp30) cc_final: 0.8175 (tp30) REVERT: L 30 SER cc_start: 0.9021 (m) cc_final: 0.8736 (t) REVERT: L 44 MET cc_start: 0.9083 (mmt) cc_final: 0.8679 (mmm) REVERT: G 16 ARG cc_start: 0.9027 (ptm-80) cc_final: 0.8505 (ptm-80) REVERT: G 35 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8283 (mm-30) REVERT: G 104 MET cc_start: 0.8551 (tmm) cc_final: 0.8284 (tmm) REVERT: G 158 PHE cc_start: 0.8539 (m-80) cc_final: 0.8336 (m-10) REVERT: Y 63 MET cc_start: 0.2562 (ppp) cc_final: 0.0271 (ttm) REVERT: Z 451 MET cc_start: 0.8139 (mmm) cc_final: 0.7934 (mmm) REVERT: Z 460 MET cc_start: 0.7906 (mmt) cc_final: 0.7604 (mmt) REVERT: Z 474 MET cc_start: 0.7390 (mtt) cc_final: 0.6752 (tpp) outliers start: 63 outliers final: 43 residues processed: 300 average time/residue: 0.2563 time to fit residues: 131.7518 Evaluate side-chains 305 residues out of total 4388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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 317 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 469 MET 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 890 ARG Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 612 ILE 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 759 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR 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 H residue 25 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain K residue 13 PHE 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 Z residue 493 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 273 optimal weight: 4.9990 chunk 457 optimal weight: 50.0000 chunk 275 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 168 optimal weight: 50.0000 chunk 92 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B1049 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 642 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 = 0.3645 r_free = 0.3645 target = 0.074075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.044431 restraints weight = 208634.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.044758 restraints weight = 105798.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.045286 restraints weight = 69100.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.045653 restraints weight = 54455.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.045773 restraints weight = 47742.529| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.6471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 42424 Z= 0.187 Angle : 0.660 13.150 57648 Z= 0.338 Chirality : 0.044 0.262 6435 Planarity : 0.004 0.086 7144 Dihedral : 14.497 176.978 6462 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 1.56 % Allowed : 14.49 % Favored : 83.95 % 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 aren not related in a simple way. whole: -0.18 (0.12), residues: 4882 helix: 1.12 (0.14), residues: 1550 sheet: -0.72 (0.19), residues: 738 loop : -0.67 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 58 TYR 0.020 0.001 TYR A 827 PHE 0.026 0.001 PHE M 526 TRP 0.013 0.001 TRP B 27 HIS 0.016 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00418 (42412) covalent geometry : angle 0.66019 (57648) hydrogen bonds : bond 0.03637 ( 1625) hydrogen bonds : angle 4.88888 ( 4483) metal coordination : bond 0.00223 ( 8) Misc. bond : bond 0.00380 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10184.57 seconds wall clock time: 176 minutes 42.14 seconds (10602.14 seconds total)