Starting phenix.real_space_refine on Sat Jun 21 07:36:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hlz_34886/06_2025/8hlz_34886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hlz_34886/06_2025/8hlz_34886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hlz_34886/06_2025/8hlz_34886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hlz_34886/06_2025/8hlz_34886.map" model { file = "/net/cci-nas-00/data/ceres_data/8hlz_34886/06_2025/8hlz_34886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hlz_34886/06_2025/8hlz_34886.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 15842 2.51 5 N 4098 2.21 5 O 4646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24718 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3020 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 7, 'TRANS': 362} Chain breaks: 1 Chain: "E" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1772 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain: "D" Number of atoms: 7567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7567 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 895} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3020 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 7, 'TRANS': 362} Chain breaks: 1 Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1772 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain: "A" Number of atoms: 7567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7567 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 895} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 14.18, per 1000 atoms: 0.57 Number of scatterers: 24718 At special positions: 0 Unit cell: (111.69, 114.975, 215.715, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4646 8.00 N 4098 7.00 C 15842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.37 Conformation dependent library (CDL) restraints added in 3.1 seconds 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5820 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 38 sheets defined 38.7% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'F' and resid 4 through 18 removed outlier: 4.572A pdb=" N LYS F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 40 removed outlier: 3.980A pdb=" N SER F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 118 removed outlier: 3.521A pdb=" N ARG F 111 " --> pdb=" O PRO F 107 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 158 removed outlier: 4.064A pdb=" N LYS F 153 " --> pdb=" O VAL F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 189 removed outlier: 4.864A pdb=" N MET F 184 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 255 removed outlier: 3.709A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 298 removed outlier: 3.622A pdb=" N VAL F 289 " --> pdb=" O THR F 285 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY F 298 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 323 Processing helix chain 'F' and resid 330 through 341 Processing helix chain 'F' and resid 341 through 349 Processing helix chain 'F' and resid 352 through 360 Processing helix chain 'F' and resid 366 through 373 removed outlier: 3.702A pdb=" N THR F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 397 through 406 removed outlier: 4.107A pdb=" N ILE F 403 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN F 406 " --> pdb=" O THR F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 425 removed outlier: 4.080A pdb=" N PHE F 410 " --> pdb=" O ASN F 406 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 19 through 38 removed outlier: 4.376A pdb=" N SER E 24 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TRP E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 54 removed outlier: 4.607A pdb=" N GLN E 52 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS E 54 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 101 removed outlier: 4.210A pdb=" N LEU E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 152 removed outlier: 3.556A pdb=" N TRP E 137 " --> pdb=" O HIS E 133 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS E 139 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE E 140 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS E 150 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS E 151 " --> pdb=" O HIS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 197 through 205 removed outlier: 3.639A pdb=" N GLU E 203 " --> pdb=" O ASN E 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 108 through 116 removed outlier: 3.628A pdb=" N PHE D 113 " --> pdb=" O ASN D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 240 through 253 Processing helix chain 'D' and resid 267 through 281 Processing helix chain 'D' and resid 330 through 339 removed outlier: 3.692A pdb=" N PHE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.534A pdb=" N PHE D 354 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 390 Processing helix chain 'D' and resid 439 through 446 removed outlier: 3.592A pdb=" N MET D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 474 removed outlier: 3.686A pdb=" N ARG D 457 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS D 461 " --> pdb=" O ARG D 457 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN D 467 " --> pdb=" O ALA D 463 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TRP D 470 " --> pdb=" O CYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 485 removed outlier: 4.243A pdb=" N ASP D 480 " --> pdb=" O GLU D 476 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'D' and resid 502 through 513 removed outlier: 3.512A pdb=" N GLU D 512 " --> pdb=" O LYS D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 561 Processing helix chain 'D' and resid 579 through 590 removed outlier: 3.692A pdb=" N LEU D 588 " --> pdb=" O ASN D 584 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 643 removed outlier: 3.778A pdb=" N LYS D 639 " --> pdb=" O ALA D 635 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS D 642 " --> pdb=" O LYS D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 666 removed outlier: 3.960A pdb=" N ASP D 654 " --> pdb=" O LYS D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 673 removed outlier: 3.796A pdb=" N GLY D 672 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 673 " --> pdb=" O GLY D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 687 Processing helix chain 'D' and resid 688 through 701 removed outlier: 3.522A pdb=" N VAL D 701 " --> pdb=" O TYR D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 782 removed outlier: 3.530A pdb=" N ALA D 771 " --> pdb=" O SER D 767 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 773 " --> pdb=" O GLU D 769 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN D 779 " --> pdb=" O GLU D 775 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER D 780 " --> pdb=" O ARG D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 854 removed outlier: 4.099A pdb=" N THR D 845 " --> pdb=" O ASN D 841 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 854 " --> pdb=" O LEU D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 882 removed outlier: 4.136A pdb=" N GLN D 863 " --> pdb=" O MET D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 979 removed outlier: 3.620A pdb=" N TYR D 971 " --> pdb=" O PHE D 967 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D 972 " --> pdb=" O TYR D 968 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D 973 " --> pdb=" O GLU D 969 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR D 976 " --> pdb=" O PHE D 972 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE D 979 " --> pdb=" O LEU D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 996 removed outlier: 3.571A pdb=" N CYS D 989 " --> pdb=" O ASN D 985 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 990 " --> pdb=" O LYS D 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 18 removed outlier: 4.572A pdb=" N LYS C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 40 removed outlier: 3.979A pdb=" N SER C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 118 removed outlier: 3.522A pdb=" N ARG C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 removed outlier: 4.065A pdb=" N LYS C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 removed outlier: 4.865A pdb=" N MET C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.711A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 298 removed outlier: 3.620A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 323 Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 341 through 349 Processing helix chain 'C' and resid 352 through 360 Processing helix chain 'C' and resid 366 through 373 removed outlier: 3.702A pdb=" N THR C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 406 removed outlier: 4.106A pdb=" N ILE C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 removed outlier: 4.080A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.378A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.688A pdb=" N LEU B 53 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 54 " --> pdb=" O ILE B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 54' Processing helix chain 'B' and resid 86 through 101 removed outlier: 4.210A pdb=" N LEU B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 152 removed outlier: 3.554A pdb=" N TRP B 137 " --> pdb=" O HIS B 133 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.640A pdb=" N GLU B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.627A pdb=" N PHE A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 281 Processing helix chain 'A' and resid 330 through 339 removed outlier: 3.692A pdb=" N PHE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.533A pdb=" N PHE A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.592A pdb=" N MET A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.686A pdb=" N ARG A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TRP A 470 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 485 removed outlier: 4.244A pdb=" N ASP A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.512A pdb=" N GLU A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 579 through 590 removed outlier: 3.694A pdb=" N LEU A 588 " --> pdb=" O ASN A 584 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 643 removed outlier: 3.777A pdb=" N LYS A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 666 removed outlier: 3.960A pdb=" N ASP A 654 " --> pdb=" O LYS A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 673 removed outlier: 3.796A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 673 " --> pdb=" O GLY A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 687 Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.523A pdb=" N VAL A 701 " --> pdb=" O TYR A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 782 removed outlier: 3.800A pdb=" N ILE A 770 " --> pdb=" O LYS A 766 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A 780 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 854 removed outlier: 4.099A pdb=" N THR A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 854 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 882 removed outlier: 4.137A pdb=" N GLN A 863 " --> pdb=" O MET A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 979 removed outlier: 3.621A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 972 " --> pdb=" O TYR A 968 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 996 removed outlier: 3.572A pdb=" N CYS A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 126 through 132 removed outlier: 6.667A pdb=" N PHE F 126 " --> pdb=" O ALA F 141 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA F 141 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ARG F 128 " --> pdb=" O GLU F 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 197 through 199 Processing sheet with id=AA3, first strand: chain 'F' and resid 244 through 245 removed outlier: 7.146A pdb=" N ILE F 238 " --> pdb=" O GLU F 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 226 through 227 Processing sheet with id=AA5, first strand: chain 'F' and resid 301 through 304 Processing sheet with id=AA6, first strand: chain 'F' and resid 375 through 380 removed outlier: 6.773A pdb=" N ARG F 376 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE F 387 " --> pdb=" O ARG F 376 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS F 378 " --> pdb=" O VAL F 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AA8, first strand: chain 'E' and resid 42 through 43 removed outlier: 3.861A pdb=" N CYS E 125 " --> pdb=" O SER E 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 116 through 120 removed outlier: 6.754A pdb=" N CYS E 63 " --> pdb=" O TYR E 156 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU E 158 " --> pdb=" O CYS E 63 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS E 65 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU E 155 " --> pdb=" O ILE E 177 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY E 179 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N CYS E 157 " --> pdb=" O GLY E 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 124 through 126 removed outlier: 6.948A pdb=" N LYS D 21 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP D 8 " --> pdb=" O TYR D 19 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR D 19 " --> pdb=" O TRP D 8 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU D 10 " --> pdb=" O PHE D 17 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE D 17 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N TYR D 140 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE D 31 " --> pdb=" O TYR D 140 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N CYS D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 38 through 43 removed outlier: 6.514A pdb=" N SER D 84 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG D 64 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA D 86 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS D 62 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N MET D 88 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ILE D 516 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG D 64 " --> pdb=" O ILE D 516 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL D 518 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE D 66 " --> pdb=" O VAL D 518 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 72 through 73 removed outlier: 6.422A pdb=" N LEU D 568 " --> pdb=" O ASP D 616 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP D 616 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY D 570 " --> pdb=" O ILE D 614 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 162 through 169 removed outlier: 3.808A pdb=" N ILE D 191 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP D 166 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER D 184 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N VAL D 237 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR D 201 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N CYS D 239 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE D 203 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AB6, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AB7, first strand: chain 'D' and resid 300 through 301 Processing sheet with id=AB8, first strand: chain 'D' and resid 355 through 360 removed outlier: 6.531A pdb=" N LYS D 416 " --> pdb=" O LYS D 408 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS D 408 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL D 418 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 548 through 549 Processing sheet with id=AC1, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.551A pdb=" N PHE D 743 " --> pdb=" O GLU D 706 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 126 through 132 removed outlier: 6.667A pdb=" N PHE C 126 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA C 141 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 197 through 199 Processing sheet with id=AC4, first strand: chain 'C' and resid 244 through 245 removed outlier: 7.146A pdb=" N ILE C 238 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AC6, first strand: chain 'C' and resid 301 through 304 Processing sheet with id=AC7, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.773A pdb=" N ARG C 376 " --> pdb=" O PHE C 387 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE C 387 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS C 378 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AC9, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.862A pdb=" N CYS B 125 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.754A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU B 158 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS B 65 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY B 179 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS B 157 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 124 through 126 removed outlier: 6.947A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.514A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.422A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 162 through 169 removed outlier: 3.807A pdb=" N ILE A 191 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 166 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AD7, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AD8, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AD9, first strand: chain 'A' and resid 355 through 360 removed outlier: 6.530A pdb=" N LYS A 416 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS A 408 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 418 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 545 through 549 Processing sheet with id=AE2, first strand: chain 'A' and resid 706 through 707 removed outlier: 3.552A pdb=" N PHE A 743 " --> pdb=" O GLU A 706 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.85 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7613 1.33 - 1.45: 4227 1.45 - 1.57: 13188 1.57 - 1.69: 4 1.69 - 1.81: 198 Bond restraints: 25230 Sorted by residual: bond pdb=" N PRO D 606 " pdb=" CD PRO D 606 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" N PRO A 606 " pdb=" CD PRO A 606 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" CA PHE C 215 " pdb=" CB PHE C 215 " ideal model delta sigma weight residual 1.534 1.588 -0.054 1.78e-02 3.16e+03 9.27e+00 bond pdb=" CA PHE F 215 " pdb=" CB PHE F 215 " ideal model delta sigma weight residual 1.534 1.586 -0.052 1.78e-02 3.16e+03 8.66e+00 bond pdb=" CB GLN A 657 " pdb=" CG GLN A 657 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.03e+00 ... (remaining 25225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 32903 2.73 - 5.45: 1018 5.45 - 8.18: 138 8.18 - 10.90: 15 10.90 - 13.63: 4 Bond angle restraints: 34078 Sorted by residual: angle pdb=" N LYS A 788 " pdb=" CA LYS A 788 " pdb=" C LYS A 788 " ideal model delta sigma weight residual 108.19 118.25 -10.06 1.29e+00 6.01e-01 6.08e+01 angle pdb=" N LYS D 788 " pdb=" CA LYS D 788 " pdb=" C LYS D 788 " ideal model delta sigma weight residual 108.19 118.24 -10.05 1.29e+00 6.01e-01 6.06e+01 angle pdb=" N ASP B 192 " pdb=" CA ASP B 192 " pdb=" C ASP B 192 " ideal model delta sigma weight residual 107.80 118.69 -10.89 1.73e+00 3.34e-01 3.96e+01 angle pdb=" C ILE B 67 " pdb=" N ASP B 68 " pdb=" CA ASP B 68 " ideal model delta sigma weight residual 122.45 110.01 12.44 2.03e+00 2.43e-01 3.75e+01 angle pdb=" C ILE E 67 " pdb=" N ASP E 68 " pdb=" CA ASP E 68 " ideal model delta sigma weight residual 122.45 110.02 12.43 2.03e+00 2.43e-01 3.75e+01 ... (remaining 34073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 12530 17.63 - 35.26: 1508 35.26 - 52.88: 821 52.88 - 70.51: 405 70.51 - 88.14: 32 Dihedral angle restraints: 15296 sinusoidal: 6298 harmonic: 8998 Sorted by residual: dihedral pdb=" CA PHE D 175 " pdb=" C PHE D 175 " pdb=" N PRO D 176 " pdb=" CA PRO D 176 " ideal model delta harmonic sigma weight residual 180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA PHE A 175 " pdb=" C PHE A 175 " pdb=" N PRO A 176 " pdb=" CA PRO A 176 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ARG A 823 " pdb=" C ARG A 823 " pdb=" N ILE A 824 " pdb=" CA ILE A 824 " ideal model delta harmonic sigma weight residual 180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 15293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2857 0.065 - 0.129: 820 0.129 - 0.194: 99 0.194 - 0.258: 17 0.258 - 0.323: 3 Chirality restraints: 3796 Sorted by residual: chirality pdb=" CA ILE D 547 " pdb=" N ILE D 547 " pdb=" C ILE D 547 " pdb=" CB ILE D 547 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE E 198 " pdb=" CA ILE E 198 " pdb=" CG1 ILE E 198 " pdb=" CG2 ILE E 198 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE B 198 " pdb=" CA ILE B 198 " pdb=" CG1 ILE B 198 " pdb=" CG2 ILE B 198 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3793 not shown) Planarity restraints: 4332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 688 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C THR D 688 " 0.075 2.00e-02 2.50e+03 pdb=" O THR D 688 " -0.028 2.00e-02 2.50e+03 pdb=" N SER D 689 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 688 " 0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C THR A 688 " -0.074 2.00e-02 2.50e+03 pdb=" O THR A 688 " 0.028 2.00e-02 2.50e+03 pdb=" N SER A 689 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 215 " 0.017 2.00e-02 2.50e+03 1.93e-02 6.53e+00 pdb=" CG PHE C 215 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 215 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 215 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 215 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 215 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 215 " 0.001 2.00e-02 2.50e+03 ... (remaining 4329 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 401 2.55 - 3.13: 20391 3.13 - 3.72: 36900 3.72 - 4.31: 51822 4.31 - 4.90: 83823 Nonbonded interactions: 193337 Sorted by model distance: nonbonded pdb=" O ASN A 716 " pdb=" OG1 THR A 717 " model vdw 1.958 3.040 nonbonded pdb=" N GLU C 109 " pdb=" OE1 GLU C 109 " model vdw 2.023 3.120 nonbonded pdb=" N GLU F 109 " pdb=" OE1 GLU F 109 " model vdw 2.026 3.120 nonbonded pdb=" O ASN D 544 " pdb=" ND2 ASN D 544 " model vdw 2.117 3.120 nonbonded pdb=" O ASN A 544 " pdb=" ND2 ASN A 544 " model vdw 2.117 3.120 ... (remaining 193332 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 55.740 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.110 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4135 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 : 0.010 0.085 25230 Z= 0.431 Angle : 1.148 13.629 34078 Z= 0.654 Chirality : 0.059 0.323 3796 Planarity : 0.006 0.057 4332 Dihedral : 21.958 88.137 9476 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 26.05 Ramachandran Plot: Outliers : 1.77 % Allowed : 11.66 % Favored : 86.58 % Rotamer: Outliers : 25.98 % Allowed : 16.15 % Favored : 57.86 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.12), residues: 3002 helix: -3.13 (0.11), residues: 1064 sheet: -2.45 (0.20), residues: 566 loop : -3.19 (0.14), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 470 HIS 0.008 0.002 HIS D 461 PHE 0.045 0.003 PHE C 215 TYR 0.028 0.003 TYR A 140 ARG 0.029 0.002 ARG B 61 Details of bonding type rmsd hydrogen bonds : bond 0.17783 ( 884) hydrogen bonds : angle 8.03541 ( 2520) covalent geometry : bond 0.00959 (25230) covalent geometry : angle 1.14835 (34078) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 727 poor density : 494 time to evaluate : 2.690 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: F 150 ASN cc_start: 0.6897 (OUTLIER) cc_final: 0.6657 (p0) REVERT: F 234 ILE cc_start: 0.6822 (pt) cc_final: 0.6440 (mm) REVERT: F 279 ASP cc_start: -0.1371 (OUTLIER) cc_final: -0.1616 (p0) REVERT: F 294 ILE cc_start: 0.4723 (mm) cc_final: 0.3359 (mm) REVERT: F 373 ASN cc_start: 0.6887 (m-40) cc_final: 0.6669 (m110) REVERT: F 380 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: E 1 MET cc_start: 0.4139 (OUTLIER) cc_final: 0.3156 (tpp) REVERT: E 50 PHE cc_start: 0.5047 (OUTLIER) cc_final: 0.4817 (m-80) REVERT: E 88 SER cc_start: 0.4430 (OUTLIER) cc_final: 0.4068 (p) REVERT: E 109 ASN cc_start: 0.6872 (OUTLIER) cc_final: 0.6544 (p0) REVERT: E 148 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7185 (tt) REVERT: E 167 ARG cc_start: 0.6776 (tpt170) cc_final: 0.6530 (mmm160) REVERT: D 177 SER cc_start: 0.7687 (OUTLIER) cc_final: 0.7405 (t) REVERT: D 271 TYR cc_start: 0.4228 (OUTLIER) cc_final: 0.3653 (m-80) REVERT: D 492 MET cc_start: 0.7975 (mmt) cc_final: 0.7490 (mmt) REVERT: D 522 THR cc_start: 0.4840 (OUTLIER) cc_final: 0.4610 (p) REVERT: D 528 TYR cc_start: 0.2872 (OUTLIER) cc_final: 0.0506 (p90) REVERT: D 544 ASN cc_start: 0.4183 (OUTLIER) cc_final: 0.3101 (m-40) REVERT: D 558 CYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6603 (t) REVERT: D 656 MET cc_start: 0.8562 (mmm) cc_final: 0.8254 (mmt) REVERT: D 765 ASP cc_start: 0.4675 (OUTLIER) cc_final: 0.4466 (t0) REVERT: D 828 THR cc_start: 0.6774 (OUTLIER) cc_final: 0.6553 (m) REVERT: D 853 MET cc_start: 0.3503 (OUTLIER) cc_final: 0.3094 (tpp) REVERT: D 858 ARG cc_start: -0.0434 (OUTLIER) cc_final: -0.2692 (ptp90) REVERT: C 33 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.7997 (p) REVERT: C 202 LEU cc_start: -0.0749 (OUTLIER) cc_final: -0.2180 (tt) REVERT: C 330 THR cc_start: 0.5935 (OUTLIER) cc_final: 0.5268 (m) REVERT: C 339 ASN cc_start: 0.6954 (t0) cc_final: 0.6595 (m-40) REVERT: B 1 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.3853 (mmt) REVERT: B 90 LYS cc_start: -0.1836 (OUTLIER) cc_final: -0.3195 (tttm) REVERT: B 178 VAL cc_start: -0.0413 (OUTLIER) cc_final: -0.0651 (p) REVERT: A 15 ASN cc_start: 0.1285 (OUTLIER) cc_final: 0.0954 (p0) REVERT: A 63 MET cc_start: -0.1508 (mtt) cc_final: -0.1881 (ttm) REVERT: A 142 CYS cc_start: 0.1883 (OUTLIER) cc_final: 0.1452 (t) REVERT: A 189 CYS cc_start: -0.1480 (OUTLIER) cc_final: -0.2204 (t) REVERT: A 191 ILE cc_start: -0.1742 (mt) cc_final: -0.2082 (mp) REVERT: A 219 ARG cc_start: -0.1345 (OUTLIER) cc_final: -0.4214 (ttp80) REVERT: A 223 ARG cc_start: -0.0074 (OUTLIER) cc_final: -0.0385 (mtt90) REVERT: A 368 MET cc_start: 0.0496 (mtp) cc_final: 0.0039 (mmt) REVERT: A 428 ILE cc_start: 0.0285 (OUTLIER) cc_final: 0.0008 (mp) REVERT: A 488 LEU cc_start: 0.3277 (OUTLIER) cc_final: 0.2706 (tp) REVERT: A 655 SER cc_start: -0.1507 (OUTLIER) cc_final: -0.2415 (t) REVERT: A 758 GLU cc_start: -0.2961 (OUTLIER) cc_final: -0.4045 (pt0) REVERT: A 799 ILE cc_start: 0.5362 (OUTLIER) cc_final: 0.4838 (mt) REVERT: A 819 SER cc_start: -0.0834 (OUTLIER) cc_final: -0.1497 (p) REVERT: A 837 LYS cc_start: -0.3887 (OUTLIER) cc_final: -0.4724 (mptt) REVERT: A 842 MET cc_start: 0.1359 (mmp) cc_final: 0.1073 (tpt) REVERT: A 847 LYS cc_start: -0.1304 (OUTLIER) cc_final: -0.2158 (tptt) REVERT: A 873 GLU cc_start: -0.1757 (OUTLIER) cc_final: -0.2344 (mt-10) REVERT: A 966 ILE cc_start: 0.3904 (OUTLIER) cc_final: 0.3611 (pt) REVERT: A 996 MET cc_start: -0.2381 (tpt) cc_final: -0.2623 (tpt) outliers start: 727 outliers final: 103 residues processed: 1089 average time/residue: 0.4384 time to fit residues: 722.6239 Evaluate side-chains 424 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 282 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 185 ARG Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 526 PHE Chi-restraints excluded: chain D residue 528 TYR Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 686 SER Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 765 ASP Chi-restraints excluded: chain D residue 819 SER Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 853 MET Chi-restraints excluded: chain D residue 855 SER Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 970 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS E 206 ASN D 141 HIS D 147 ASN ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN D 225 GLN D 562 ASN D 585 GLN D 600 HIS D 797 ASN D 937 ASN C 146 GLN C 208 GLN C 397 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS A 147 ASN A 336 GLN A 413 ASN A 797 ASN A 816 ASN A 862 ASN A 937 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.189083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.152154 restraints weight = 85277.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.150997 restraints weight = 43267.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.152504 restraints weight = 32687.123| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25230 Z= 0.179 Angle : 0.818 12.541 34078 Z= 0.429 Chirality : 0.050 0.312 3796 Planarity : 0.006 0.072 4332 Dihedral : 11.386 100.717 3621 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.56 % Favored : 91.77 % Rotamer: Outliers : 8.18 % Allowed : 24.20 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.14), residues: 3002 helix: -1.54 (0.14), residues: 1080 sheet: -1.39 (0.22), residues: 524 loop : -2.78 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 470 HIS 0.005 0.001 HIS D 185 PHE 0.027 0.002 PHE D 385 TYR 0.025 0.002 TYR A 681 ARG 0.022 0.001 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.05488 ( 884) hydrogen bonds : angle 6.02726 ( 2520) covalent geometry : bond 0.00380 (25230) covalent geometry : angle 0.81774 (34078) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 308 time to evaluate : 2.968 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: F 246 LEU cc_start: 0.6670 (mt) cc_final: 0.6017 (tp) REVERT: F 275 LEU cc_start: 0.7841 (tp) cc_final: 0.7098 (pp) REVERT: F 291 LYS cc_start: 0.8409 (pptt) cc_final: 0.8124 (tppt) REVERT: F 294 ILE cc_start: 0.6124 (mm) cc_final: 0.5757 (mm) REVERT: F 380 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: E 1 MET cc_start: 0.3669 (mmp) cc_final: 0.3329 (tpt) REVERT: E 142 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7400 (mmmt) REVERT: E 167 ARG cc_start: 0.7048 (tpt170) cc_final: 0.6669 (mmm160) REVERT: E 181 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6786 (t-170) REVERT: D 187 SER cc_start: 0.5395 (OUTLIER) cc_final: 0.4985 (m) REVERT: D 207 MET cc_start: 0.5451 (ttt) cc_final: 0.5189 (mtp) REVERT: D 211 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6765 (pp30) REVERT: D 271 TYR cc_start: 0.5567 (OUTLIER) cc_final: 0.4168 (m-80) REVERT: D 357 MET cc_start: 0.8052 (mpp) cc_final: 0.7659 (mmm) REVERT: D 369 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.6263 (t) REVERT: D 609 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6871 (pt) REVERT: D 711 MET cc_start: 0.4440 (tmm) cc_final: 0.4023 (tmm) REVERT: D 806 TYR cc_start: 0.7688 (m-80) cc_final: 0.7389 (m-80) REVERT: D 808 THR cc_start: 0.6680 (p) cc_final: 0.6461 (p) REVERT: D 828 THR cc_start: 0.7557 (OUTLIER) cc_final: 0.7272 (m) REVERT: D 853 MET cc_start: 0.5187 (OUTLIER) cc_final: 0.4661 (tpp) REVERT: D 858 ARG cc_start: -0.0932 (OUTLIER) cc_final: -0.2457 (ptp90) REVERT: D 891 MET cc_start: 0.5367 (mpp) cc_final: 0.5162 (mpp) REVERT: D 932 TYR cc_start: 0.5303 (OUTLIER) cc_final: 0.4516 (m-80) REVERT: C 20 LEU cc_start: 0.5175 (OUTLIER) cc_final: 0.4878 (tp) REVERT: C 29 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5832 (tp30) REVERT: C 33 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8349 (p) REVERT: C 122 ASN cc_start: 0.5250 (m-40) cc_final: 0.4706 (t0) REVERT: C 339 ASN cc_start: 0.6925 (t0) cc_final: 0.6258 (m-40) REVERT: C 390 GLU cc_start: 0.4881 (OUTLIER) cc_final: 0.4534 (mp0) REVERT: B 23 MET cc_start: 0.2684 (ppp) cc_final: 0.2210 (ptp) REVERT: B 178 VAL cc_start: 0.0606 (OUTLIER) cc_final: 0.0394 (p) REVERT: A 88 MET cc_start: 0.0337 (ttp) cc_final: 0.0116 (ptt) REVERT: A 158 ILE cc_start: -0.2435 (OUTLIER) cc_final: -0.2636 (mm) REVERT: A 210 GLU cc_start: 0.5289 (OUTLIER) cc_final: 0.4962 (tp30) REVERT: A 219 ARG cc_start: -0.4684 (OUTLIER) cc_final: -0.5012 (ttp-170) REVERT: A 223 ARG cc_start: 0.3192 (OUTLIER) cc_final: 0.0943 (mmt90) REVERT: A 332 TYR cc_start: 0.7153 (t80) cc_final: 0.6864 (t80) REVERT: A 356 CYS cc_start: 0.2324 (OUTLIER) cc_final: 0.1579 (p) REVERT: A 428 ILE cc_start: 0.1991 (OUTLIER) cc_final: 0.1700 (mp) REVERT: A 698 LEU cc_start: 0.7658 (tp) cc_final: 0.7203 (pp) REVERT: A 819 SER cc_start: 0.2109 (OUTLIER) cc_final: 0.1424 (p) REVERT: A 837 LYS cc_start: -0.5827 (OUTLIER) cc_final: -0.6329 (mttt) REVERT: A 842 MET cc_start: 0.1615 (mmp) cc_final: 0.1002 (tpt) REVERT: A 859 MET cc_start: 0.6573 (tpp) cc_final: 0.5448 (tmm) outliers start: 229 outliers final: 116 residues processed: 506 average time/residue: 0.4025 time to fit residues: 319.0647 Evaluate side-chains 378 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 238 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 181 HIS Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 853 MET Chi-restraints excluded: chain D residue 855 SER Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 962 SER Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 970 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 128 optimal weight: 0.4980 chunk 162 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 193 optimal weight: 0.0870 chunk 127 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 292 optimal weight: 10.0000 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 146 GLN ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN E 181 HIS D 75 ASN D 141 HIS ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 HIS A 336 GLN A 448 ASN A 963 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.188035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.150971 restraints weight = 83755.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.150470 restraints weight = 48841.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.151105 restraints weight = 32813.158| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5842 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25230 Z= 0.143 Angle : 0.698 11.403 34078 Z= 0.367 Chirality : 0.047 0.275 3796 Planarity : 0.005 0.058 4332 Dihedral : 9.038 86.344 3467 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.33 % Favored : 92.07 % Rotamer: Outliers : 6.25 % Allowed : 24.59 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.14), residues: 3002 helix: -0.94 (0.15), residues: 1084 sheet: -1.06 (0.23), residues: 506 loop : -2.53 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 19 HIS 0.013 0.001 HIS E 181 PHE 0.020 0.002 PHE A 791 TYR 0.021 0.002 TYR A 190 ARG 0.007 0.001 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 884) hydrogen bonds : angle 5.54921 ( 2520) covalent geometry : bond 0.00286 (25230) covalent geometry : angle 0.69832 (34078) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 267 time to evaluate : 3.007 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: F 234 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8009 (pt) REVERT: F 246 LEU cc_start: 0.6645 (mt) cc_final: 0.6235 (tp) REVERT: F 260 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5915 (pp20) REVERT: F 294 ILE cc_start: 0.6023 (mm) cc_final: 0.5696 (mm) REVERT: F 323 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7536 (mt) REVERT: F 380 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: E 1 MET cc_start: 0.3553 (mmp) cc_final: 0.3214 (tpt) REVERT: E 109 ASN cc_start: 0.6241 (OUTLIER) cc_final: 0.5892 (p0) REVERT: E 142 LYS cc_start: 0.7881 (mmmt) cc_final: 0.7285 (mmmt) REVERT: E 167 ARG cc_start: 0.7073 (tpt170) cc_final: 0.6489 (mmm160) REVERT: D 211 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6443 (pp30) REVERT: D 271 TYR cc_start: 0.5684 (OUTLIER) cc_final: 0.4213 (m-80) REVERT: D 318 PHE cc_start: 0.7416 (m-80) cc_final: 0.7172 (m-80) REVERT: D 512 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: D 604 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6244 (mtp85) REVERT: D 828 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.6867 (m) REVERT: D 853 MET cc_start: 0.5397 (OUTLIER) cc_final: 0.4858 (tpp) REVERT: D 858 ARG cc_start: -0.1079 (OUTLIER) cc_final: -0.2541 (ptp90) REVERT: D 932 TYR cc_start: 0.5478 (OUTLIER) cc_final: 0.4771 (m-80) REVERT: D 960 LEU cc_start: -0.0122 (OUTLIER) cc_final: -0.1947 (tp) REVERT: C 1 MET cc_start: 0.4193 (tmm) cc_final: 0.3223 (mmm) REVERT: C 29 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5932 (tp30) REVERT: C 122 ASN cc_start: 0.5147 (m-40) cc_final: 0.4451 (p0) REVERT: C 179 GLU cc_start: 0.8298 (tp30) cc_final: 0.7960 (tp30) REVERT: C 339 ASN cc_start: 0.6959 (t0) cc_final: 0.6276 (m-40) REVERT: C 376 ARG cc_start: 0.3696 (mmt180) cc_final: 0.2255 (tpt170) REVERT: C 390 GLU cc_start: 0.4682 (OUTLIER) cc_final: 0.4415 (mp0) REVERT: B 1 MET cc_start: 0.7305 (mmp) cc_final: 0.6531 (tpp) REVERT: B 23 MET cc_start: 0.2868 (ppp) cc_final: 0.2473 (ptp) REVERT: B 57 LEU cc_start: 0.6905 (mt) cc_final: 0.5898 (mt) REVERT: A 158 ILE cc_start: -0.2479 (OUTLIER) cc_final: -0.3165 (pt) REVERT: A 210 GLU cc_start: 0.5180 (OUTLIER) cc_final: 0.4840 (tp30) REVERT: A 223 ARG cc_start: 0.2559 (OUTLIER) cc_final: 0.0548 (mmt90) REVERT: A 298 CYS cc_start: 0.4978 (p) cc_final: 0.4580 (m) REVERT: A 428 ILE cc_start: 0.2209 (OUTLIER) cc_final: 0.1943 (mp) REVERT: A 448 ASN cc_start: 0.7075 (OUTLIER) cc_final: 0.6787 (p0) REVERT: A 469 LEU cc_start: 0.5943 (mm) cc_final: 0.5430 (tt) REVERT: A 698 LEU cc_start: 0.7609 (tp) cc_final: 0.7192 (pp) REVERT: A 815 SER cc_start: 0.7238 (m) cc_final: 0.7033 (m) REVERT: A 837 LYS cc_start: -0.6256 (OUTLIER) cc_final: -0.6691 (mttt) REVERT: A 842 MET cc_start: 0.1295 (mmp) cc_final: 0.0687 (tpt) REVERT: A 853 MET cc_start: 0.1814 (mmm) cc_final: 0.1433 (mmp) REVERT: A 859 MET cc_start: 0.6661 (tpp) cc_final: 0.5462 (tmm) REVERT: A 891 MET cc_start: 0.1957 (OUTLIER) cc_final: 0.1612 (mmm) REVERT: A 892 LEU cc_start: 0.0849 (OUTLIER) cc_final: 0.0560 (tt) outliers start: 175 outliers final: 90 residues processed: 418 average time/residue: 0.3733 time to fit residues: 243.0907 Evaluate side-chains 350 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 236 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 604 ARG Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 671 MET Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 853 MET Chi-restraints excluded: chain D residue 855 SER Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 963 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 65 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 275 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 245 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 281 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 ASN F 321 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS A 352 ASN ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.185515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.148699 restraints weight = 84950.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.147473 restraints weight = 44233.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.149053 restraints weight = 33063.541| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25230 Z= 0.150 Angle : 0.675 11.460 34078 Z= 0.357 Chirality : 0.046 0.222 3796 Planarity : 0.005 0.054 4332 Dihedral : 8.022 88.557 3429 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.26 % Favored : 92.24 % Rotamer: Outliers : 6.22 % Allowed : 24.12 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 3002 helix: -0.71 (0.15), residues: 1074 sheet: -0.99 (0.23), residues: 514 loop : -2.42 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 470 HIS 0.005 0.001 HIS D 141 PHE 0.023 0.002 PHE F 152 TYR 0.034 0.002 TYR A 637 ARG 0.006 0.001 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 884) hydrogen bonds : angle 5.40293 ( 2520) covalent geometry : bond 0.00323 (25230) covalent geometry : angle 0.67533 (34078) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 254 time to evaluate : 2.877 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: F 260 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5777 (pp20) REVERT: F 294 ILE cc_start: 0.6245 (mm) cc_final: 0.5946 (mm) REVERT: F 373 ASN cc_start: 0.8351 (m-40) cc_final: 0.7581 (m110) REVERT: F 375 MET cc_start: 0.6914 (mtp) cc_final: 0.6236 (mtp) REVERT: F 380 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: F 390 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8479 (mm-30) REVERT: E 109 ASN cc_start: 0.6173 (OUTLIER) cc_final: 0.5502 (p0) REVERT: E 142 LYS cc_start: 0.7647 (mmmt) cc_final: 0.7124 (mmmt) REVERT: E 167 ARG cc_start: 0.7176 (tpt170) cc_final: 0.6976 (mmm160) REVERT: D 70 GLU cc_start: 0.5710 (mt-10) cc_final: 0.5389 (mt-10) REVERT: D 299 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7066 (mm) REVERT: D 357 MET cc_start: 0.8136 (mmm) cc_final: 0.7580 (tpp) REVERT: D 492 MET cc_start: 0.8210 (mmt) cc_final: 0.7923 (mmt) REVERT: D 611 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5884 (tt0) REVERT: D 711 MET cc_start: 0.4587 (tmm) cc_final: 0.4109 (tmm) REVERT: D 716 ASN cc_start: 0.5995 (OUTLIER) cc_final: 0.5508 (p0) REVERT: D 828 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.7175 (m) REVERT: D 853 MET cc_start: 0.5689 (OUTLIER) cc_final: 0.5190 (tpp) REVERT: D 858 ARG cc_start: -0.1819 (OUTLIER) cc_final: -0.3368 (ptp90) REVERT: D 859 MET cc_start: 0.6990 (tpp) cc_final: 0.6566 (tpt) REVERT: D 891 MET cc_start: 0.3545 (mpp) cc_final: 0.3295 (tpp) REVERT: D 932 TYR cc_start: 0.5501 (OUTLIER) cc_final: 0.4898 (m-80) REVERT: D 960 LEU cc_start: 0.0040 (OUTLIER) cc_final: -0.2014 (tp) REVERT: C 29 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5808 (tp30) REVERT: C 122 ASN cc_start: 0.4613 (m-40) cc_final: 0.4290 (p0) REVERT: C 177 ASP cc_start: 0.6901 (OUTLIER) cc_final: 0.6664 (m-30) REVERT: C 179 GLU cc_start: 0.8256 (tp30) cc_final: 0.7844 (tp30) REVERT: C 183 ILE cc_start: 0.8512 (pp) cc_final: 0.8237 (pp) REVERT: C 249 ASP cc_start: 0.6257 (p0) cc_final: 0.5284 (p0) REVERT: C 284 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5676 (tp30) REVERT: C 339 ASN cc_start: 0.6618 (t0) cc_final: 0.6030 (m-40) REVERT: C 376 ARG cc_start: 0.3850 (mmt180) cc_final: 0.2400 (tpt170) REVERT: C 390 GLU cc_start: 0.4816 (OUTLIER) cc_final: 0.4591 (mp0) REVERT: C 414 PHE cc_start: 0.5619 (OUTLIER) cc_final: 0.5218 (m-80) REVERT: B 1 MET cc_start: 0.7113 (mmp) cc_final: 0.6379 (tpp) REVERT: B 23 MET cc_start: 0.3460 (ppp) cc_final: 0.2981 (ptp) REVERT: A 21 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.6137 (tmtt) REVERT: A 34 PHE cc_start: 0.2481 (OUTLIER) cc_final: 0.1738 (t80) REVERT: A 63 MET cc_start: -0.2576 (ttm) cc_final: -0.2934 (ttt) REVERT: A 158 ILE cc_start: -0.3049 (OUTLIER) cc_final: -0.3629 (pt) REVERT: A 191 ILE cc_start: 0.1633 (mp) cc_final: 0.1176 (mp) REVERT: A 192 ASP cc_start: 0.5710 (t0) cc_final: 0.4659 (p0) REVERT: A 210 GLU cc_start: 0.4885 (OUTLIER) cc_final: 0.4649 (tp30) REVERT: A 223 ARG cc_start: 0.2937 (OUTLIER) cc_final: 0.0966 (mmt90) REVERT: A 230 MET cc_start: -0.2655 (ttp) cc_final: -0.3122 (ttm) REVERT: A 298 CYS cc_start: 0.5143 (p) cc_final: 0.4874 (m) REVERT: A 351 LYS cc_start: 0.6545 (tptp) cc_final: 0.6138 (mmmt) REVERT: A 407 ARG cc_start: 0.5596 (mtt180) cc_final: 0.3794 (ptt90) REVERT: A 596 TYR cc_start: 0.2901 (m-80) cc_final: 0.2646 (m-10) REVERT: A 698 LEU cc_start: 0.7582 (tp) cc_final: 0.7309 (pp) REVERT: A 788 LYS cc_start: 0.7619 (tppt) cc_final: 0.7282 (tppt) REVERT: A 815 SER cc_start: 0.7341 (m) cc_final: 0.7124 (m) REVERT: A 842 MET cc_start: 0.0994 (mmp) cc_final: 0.0456 (tpt) REVERT: A 859 MET cc_start: 0.6882 (tpp) cc_final: 0.5850 (tmm) REVERT: A 892 LEU cc_start: 0.0727 (OUTLIER) cc_final: 0.0465 (tt) outliers start: 174 outliers final: 96 residues processed: 399 average time/residue: 0.3653 time to fit residues: 229.1352 Evaluate side-chains 343 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 225 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 381 ASN Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 765 ASP Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 815 SER Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 853 MET Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 963 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 126 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 264 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 0.0050 chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN A 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.185540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.151016 restraints weight = 84462.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.149373 restraints weight = 44459.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.150274 restraints weight = 33574.684| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25230 Z= 0.127 Angle : 0.648 10.496 34078 Z= 0.340 Chirality : 0.045 0.236 3796 Planarity : 0.004 0.053 4332 Dihedral : 7.472 88.782 3409 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.16 % Favored : 92.37 % Rotamer: Outliers : 5.47 % Allowed : 24.73 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 3002 helix: -0.49 (0.15), residues: 1076 sheet: -1.16 (0.22), residues: 552 loop : -2.26 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 470 HIS 0.024 0.001 HIS B 147 PHE 0.023 0.002 PHE D 714 TYR 0.030 0.002 TYR E 15 ARG 0.010 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 884) hydrogen bonds : angle 5.28290 ( 2520) covalent geometry : bond 0.00269 (25230) covalent geometry : angle 0.64798 (34078) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 239 time to evaluate : 2.618 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: F 174 THR cc_start: 0.0683 (OUTLIER) cc_final: 0.0463 (p) REVERT: F 184 MET cc_start: 0.4482 (tpp) cc_final: 0.4169 (tpt) REVERT: F 294 ILE cc_start: 0.6270 (mm) cc_final: 0.5947 (mm) REVERT: F 373 ASN cc_start: 0.8327 (m-40) cc_final: 0.7553 (m110) REVERT: F 375 MET cc_start: 0.7019 (mtp) cc_final: 0.6086 (mtp) REVERT: F 380 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: F 390 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8408 (mm-30) REVERT: F 393 ASN cc_start: 0.8937 (m-40) cc_final: 0.8707 (m-40) REVERT: E 167 ARG cc_start: 0.7233 (tpt170) cc_final: 0.7025 (mmm160) REVERT: D 70 GLU cc_start: 0.5671 (mt-10) cc_final: 0.5430 (mt-10) REVERT: D 122 ASP cc_start: 0.8055 (t0) cc_final: 0.7793 (t0) REVERT: D 299 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7059 (mm) REVERT: D 357 MET cc_start: 0.8304 (mmm) cc_final: 0.8007 (tpp) REVERT: D 492 MET cc_start: 0.8212 (mmt) cc_final: 0.7857 (mmt) REVERT: D 605 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7098 (tt) REVERT: D 611 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.5920 (tt0) REVERT: D 828 THR cc_start: 0.7053 (OUTLIER) cc_final: 0.6737 (m) REVERT: D 853 MET cc_start: 0.5527 (ttp) cc_final: 0.5222 (tpp) REVERT: D 858 ARG cc_start: -0.1795 (OUTLIER) cc_final: -0.3445 (ptp90) REVERT: D 891 MET cc_start: 0.4131 (mpp) cc_final: 0.3888 (tpp) REVERT: D 932 TYR cc_start: 0.5474 (OUTLIER) cc_final: 0.4897 (m-80) REVERT: C 29 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5753 (tp30) REVERT: C 249 ASP cc_start: 0.5653 (p0) cc_final: 0.5100 (p0) REVERT: C 284 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5477 (tp30) REVERT: C 339 ASN cc_start: 0.6663 (t0) cc_final: 0.6304 (m-40) REVERT: C 355 ASP cc_start: 0.8135 (m-30) cc_final: 0.7929 (p0) REVERT: C 376 ARG cc_start: 0.4112 (mmt180) cc_final: 0.2427 (tpt170) REVERT: C 414 PHE cc_start: 0.5360 (OUTLIER) cc_final: 0.4933 (m-80) REVERT: B 23 MET cc_start: 0.4166 (ppp) cc_final: 0.3455 (ptp) REVERT: A 34 PHE cc_start: 0.2666 (OUTLIER) cc_final: 0.1899 (t80) REVERT: A 158 ILE cc_start: -0.3347 (OUTLIER) cc_final: -0.3822 (pt) REVERT: A 191 ILE cc_start: 0.1262 (mp) cc_final: 0.0879 (mp) REVERT: A 192 ASP cc_start: 0.5518 (t0) cc_final: 0.4535 (p0) REVERT: A 223 ARG cc_start: 0.2463 (OUTLIER) cc_final: 0.0429 (mmt90) REVERT: A 230 MET cc_start: -0.2381 (ttp) cc_final: -0.3038 (ttm) REVERT: A 298 CYS cc_start: 0.5143 (p) cc_final: 0.4799 (m) REVERT: A 351 LYS cc_start: 0.6391 (tptp) cc_final: 0.5917 (mmmt) REVERT: A 356 CYS cc_start: 0.1598 (OUTLIER) cc_final: 0.0887 (p) REVERT: A 656 MET cc_start: -0.0908 (mmp) cc_final: -0.1212 (mmp) REVERT: A 815 SER cc_start: 0.7333 (m) cc_final: 0.7078 (m) REVERT: A 842 MET cc_start: 0.0948 (mmp) cc_final: 0.0335 (tpt) REVERT: A 859 MET cc_start: 0.7059 (tpp) cc_final: 0.6126 (tmm) outliers start: 153 outliers final: 102 residues processed: 371 average time/residue: 0.3496 time to fit residues: 205.6091 Evaluate side-chains 337 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 220 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 381 ASN Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 181 HIS Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 964 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 285 optimal weight: 9.9990 chunk 186 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 381 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN E 211 ASN D 48 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 ASN ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.182516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.146639 restraints weight = 83664.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.143952 restraints weight = 45774.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.144564 restraints weight = 37152.919| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25230 Z= 0.162 Angle : 0.684 11.317 34078 Z= 0.359 Chirality : 0.047 0.245 3796 Planarity : 0.005 0.050 4332 Dihedral : 7.238 89.462 3397 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.59 % Favored : 91.94 % Rotamer: Outliers : 5.93 % Allowed : 24.91 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.15), residues: 3002 helix: -0.57 (0.15), residues: 1090 sheet: -0.99 (0.23), residues: 506 loop : -2.21 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 470 HIS 0.007 0.001 HIS B 147 PHE 0.026 0.002 PHE F 152 TYR 0.029 0.002 TYR A 271 ARG 0.010 0.001 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 884) hydrogen bonds : angle 5.32350 ( 2520) covalent geometry : bond 0.00362 (25230) covalent geometry : angle 0.68428 (34078) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 229 time to evaluate : 3.298 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: F 1 MET cc_start: 0.0269 (tpp) cc_final: -0.1355 (tmm) REVERT: F 306 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7363 (mtmm) REVERT: F 380 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: F 390 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8433 (mm-30) REVERT: F 393 ASN cc_start: 0.9001 (m-40) cc_final: 0.8769 (m-40) REVERT: E 167 ARG cc_start: 0.7333 (tpt170) cc_final: 0.7090 (mmm160) REVERT: E 177 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6753 (mp) REVERT: D 70 GLU cc_start: 0.5683 (mt-10) cc_final: 0.5400 (mt-10) REVERT: D 357 MET cc_start: 0.8448 (mmm) cc_final: 0.8173 (tpp) REVERT: D 492 MET cc_start: 0.8254 (mmt) cc_final: 0.7945 (mmt) REVERT: D 605 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6883 (tt) REVERT: D 611 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5857 (tt0) REVERT: D 711 MET cc_start: 0.4779 (tmm) cc_final: 0.4564 (tmm) REVERT: D 828 THR cc_start: 0.7370 (OUTLIER) cc_final: 0.7102 (m) REVERT: D 853 MET cc_start: 0.5908 (OUTLIER) cc_final: 0.5443 (tpp) REVERT: D 858 ARG cc_start: -0.1351 (OUTLIER) cc_final: -0.3276 (ptp90) REVERT: D 859 MET cc_start: 0.7167 (tpp) cc_final: 0.6873 (tpp) REVERT: C 29 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6075 (tp30) REVERT: C 339 ASN cc_start: 0.6776 (t0) cc_final: 0.6170 (m-40) REVERT: C 376 ARG cc_start: 0.4617 (mmt180) cc_final: 0.2557 (tpt170) REVERT: C 414 PHE cc_start: 0.5525 (OUTLIER) cc_final: 0.5130 (m-80) REVERT: B 23 MET cc_start: 0.4107 (ppp) cc_final: 0.3151 (ptp) REVERT: A 158 ILE cc_start: -0.3120 (OUTLIER) cc_final: -0.3608 (pt) REVERT: A 180 ILE cc_start: 0.0678 (OUTLIER) cc_final: 0.0382 (mm) REVERT: A 223 ARG cc_start: 0.3178 (OUTLIER) cc_final: 0.1376 (mmt90) REVERT: A 230 MET cc_start: -0.2264 (ttp) cc_final: -0.3007 (ttm) REVERT: A 636 ARG cc_start: 0.5848 (tmm-80) cc_final: 0.5553 (tmm-80) REVERT: A 640 MET cc_start: -0.0144 (OUTLIER) cc_final: -0.1260 (ppp) REVERT: A 741 TYR cc_start: 0.4554 (m-80) cc_final: 0.3478 (m-80) REVERT: A 815 SER cc_start: 0.7433 (m) cc_final: 0.7199 (m) REVERT: A 842 MET cc_start: 0.0898 (mmp) cc_final: 0.0405 (tpt) REVERT: A 859 MET cc_start: 0.6822 (tpp) cc_final: 0.5957 (tmm) REVERT: A 996 MET cc_start: 0.0702 (ttm) cc_final: -0.1238 (mmt) outliers start: 166 outliers final: 110 residues processed: 377 average time/residue: 0.3660 time to fit residues: 217.1591 Evaluate side-chains 323 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 199 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 306 LYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 181 HIS Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 853 MET Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 964 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 94 optimal weight: 0.0040 chunk 78 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 208 optimal weight: 30.0000 chunk 100 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 205 optimal weight: 0.0770 chunk 175 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 255 optimal weight: 9.9990 overall best weight: 0.9354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 GLN F 261 HIS ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.184080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.147220 restraints weight = 83780.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.145625 restraints weight = 41600.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.146614 restraints weight = 30294.985| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.6605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25230 Z= 0.118 Angle : 0.634 11.770 34078 Z= 0.333 Chirality : 0.045 0.220 3796 Planarity : 0.004 0.051 4332 Dihedral : 6.658 90.738 3387 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.63 % Favored : 92.90 % Rotamer: Outliers : 4.61 % Allowed : 26.20 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 3002 helix: -0.23 (0.15), residues: 1072 sheet: -0.65 (0.23), residues: 518 loop : -2.11 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 43 HIS 0.007 0.001 HIS B 147 PHE 0.022 0.001 PHE F 152 TYR 0.035 0.001 TYR E 15 ARG 0.008 0.000 ARG F 358 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 884) hydrogen bonds : angle 5.15277 ( 2520) covalent geometry : bond 0.00249 (25230) covalent geometry : angle 0.63374 (34078) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 231 time to evaluate : 2.874 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: F 1 MET cc_start: 0.0201 (tpp) cc_final: -0.1385 (tmm) REVERT: F 358 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6771 (ttt-90) REVERT: F 367 ASP cc_start: 0.7674 (p0) cc_final: 0.7363 (p0) REVERT: F 373 ASN cc_start: 0.8450 (m-40) cc_final: 0.7762 (m110) REVERT: F 390 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8432 (mm-30) REVERT: F 393 ASN cc_start: 0.9082 (m-40) cc_final: 0.8880 (m-40) REVERT: E 167 ARG cc_start: 0.7322 (tpt170) cc_final: 0.7064 (mmm160) REVERT: E 177 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6831 (mp) REVERT: D 70 GLU cc_start: 0.5657 (mt-10) cc_final: 0.5215 (mt-10) REVERT: D 283 LYS cc_start: 0.4582 (OUTLIER) cc_final: 0.3831 (mtmt) REVERT: D 492 MET cc_start: 0.8283 (mmt) cc_final: 0.7830 (mtt) REVERT: D 605 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6838 (tt) REVERT: D 611 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5484 (tt0) REVERT: D 800 MET cc_start: 0.5874 (tpt) cc_final: 0.5421 (tpt) REVERT: D 828 THR cc_start: 0.7245 (OUTLIER) cc_final: 0.6983 (m) REVERT: D 853 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5482 (tpp) REVERT: D 858 ARG cc_start: -0.1413 (OUTLIER) cc_final: -0.3417 (ptp-110) REVERT: C 1 MET cc_start: 0.4922 (tmm) cc_final: 0.4566 (tmm) REVERT: C 29 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6162 (tp30) REVERT: C 339 ASN cc_start: 0.6370 (t0) cc_final: 0.5549 (m-40) REVERT: C 376 ARG cc_start: 0.4506 (mmt180) cc_final: 0.2419 (tpt170) REVERT: C 414 PHE cc_start: 0.5372 (OUTLIER) cc_final: 0.4935 (m-80) REVERT: B 23 MET cc_start: 0.3971 (ppp) cc_final: 0.3074 (ptp) REVERT: B 158 LEU cc_start: 0.5078 (OUTLIER) cc_final: 0.4662 (mm) REVERT: A 158 ILE cc_start: -0.3280 (OUTLIER) cc_final: -0.3679 (pt) REVERT: A 230 MET cc_start: -0.2628 (ttp) cc_final: -0.3269 (ttm) REVERT: A 356 CYS cc_start: 0.1719 (OUTLIER) cc_final: 0.0898 (p) REVERT: A 407 ARG cc_start: 0.5702 (mtt180) cc_final: 0.3759 (ptt90) REVERT: A 490 GLN cc_start: 0.4442 (mp10) cc_final: 0.3000 (mp10) REVERT: A 640 MET cc_start: -0.0290 (OUTLIER) cc_final: -0.1171 (ppp) REVERT: A 741 TYR cc_start: 0.4561 (m-80) cc_final: 0.3467 (m-80) REVERT: A 800 MET cc_start: 0.3372 (ttt) cc_final: 0.3014 (ppp) REVERT: A 815 SER cc_start: 0.7508 (m) cc_final: 0.7282 (m) REVERT: A 842 MET cc_start: 0.0784 (mmp) cc_final: 0.0401 (tpt) REVERT: A 859 MET cc_start: 0.6765 (tpp) cc_final: 0.5882 (tmm) REVERT: A 891 MET cc_start: -0.0681 (ptt) cc_final: -0.0966 (ptt) REVERT: A 996 MET cc_start: 0.0197 (ttm) cc_final: -0.1610 (mmt) outliers start: 129 outliers final: 85 residues processed: 344 average time/residue: 0.3994 time to fit residues: 214.2406 Evaluate side-chains 307 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 208 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 181 HIS Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 853 MET Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 43 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 234 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 225 optimal weight: 2.9990 chunk 195 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 GLN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 HIS ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A 583 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.178778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.142160 restraints weight = 83064.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.139433 restraints weight = 47939.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.140376 restraints weight = 36904.050| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 25230 Z= 0.222 Angle : 0.773 12.667 34078 Z= 0.405 Chirality : 0.049 0.250 3796 Planarity : 0.005 0.051 4332 Dihedral : 6.865 92.008 3374 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.29 % Favored : 91.24 % Rotamer: Outliers : 5.00 % Allowed : 26.52 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 3002 helix: -0.62 (0.15), residues: 1084 sheet: -0.86 (0.23), residues: 516 loop : -2.26 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 470 HIS 0.007 0.002 HIS B 147 PHE 0.030 0.002 PHE F 152 TYR 0.027 0.002 TYR A 668 ARG 0.014 0.001 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 884) hydrogen bonds : angle 5.57643 ( 2520) covalent geometry : bond 0.00498 (25230) covalent geometry : angle 0.77282 (34078) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 212 time to evaluate : 2.814 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: F 1 MET cc_start: 0.0068 (tpp) cc_final: -0.1494 (tmm) REVERT: F 138 MET cc_start: 0.7222 (ttm) cc_final: 0.6714 (mpp) REVERT: F 373 ASN cc_start: 0.8474 (m-40) cc_final: 0.7998 (m-40) REVERT: F 375 MET cc_start: 0.6955 (mmm) cc_final: 0.6577 (mmm) REVERT: F 390 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8441 (mm-30) REVERT: E 23 MET cc_start: 0.1753 (ttp) cc_final: 0.1484 (ttm) REVERT: E 167 ARG cc_start: 0.7581 (tpt170) cc_final: 0.7304 (mmm160) REVERT: E 181 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.6959 (t-170) REVERT: D 60 MET cc_start: 0.7754 (mpp) cc_final: 0.7329 (mpp) REVERT: D 70 GLU cc_start: 0.5918 (mt-10) cc_final: 0.5514 (mt-10) REVERT: D 357 MET cc_start: 0.8379 (tpp) cc_final: 0.8119 (tpp) REVERT: D 492 MET cc_start: 0.8304 (mmt) cc_final: 0.7934 (mmt) REVERT: D 608 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8280 (pp) REVERT: D 828 THR cc_start: 0.7400 (OUTLIER) cc_final: 0.7147 (m) REVERT: D 853 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.5782 (tpp) REVERT: D 858 ARG cc_start: -0.0586 (OUTLIER) cc_final: -0.3484 (ptp90) REVERT: D 859 MET cc_start: 0.6573 (tpp) cc_final: 0.6263 (tpp) REVERT: D 960 LEU cc_start: 0.1746 (OUTLIER) cc_final: 0.1429 (pp) REVERT: C 1 MET cc_start: 0.5410 (tmm) cc_final: 0.5052 (tmm) REVERT: C 25 SER cc_start: 0.7409 (t) cc_final: 0.6210 (p) REVERT: C 29 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5996 (tp30) REVERT: C 339 ASN cc_start: 0.6373 (t0) cc_final: 0.5666 (m-40) REVERT: C 376 ARG cc_start: 0.4417 (mmt180) cc_final: 0.2379 (tpt170) REVERT: C 414 PHE cc_start: 0.5476 (OUTLIER) cc_final: 0.5017 (m-80) REVERT: B 23 MET cc_start: 0.3824 (ppp) cc_final: 0.3040 (ptp) REVERT: B 158 LEU cc_start: 0.5402 (OUTLIER) cc_final: 0.4988 (mm) REVERT: A 158 ILE cc_start: -0.3118 (OUTLIER) cc_final: -0.3416 (pt) REVERT: A 223 ARG cc_start: 0.3501 (OUTLIER) cc_final: 0.1401 (mmt90) REVERT: A 230 MET cc_start: -0.2130 (ttp) cc_final: -0.2773 (ttm) REVERT: A 298 CYS cc_start: 0.5005 (m) cc_final: 0.4698 (p) REVERT: A 351 LYS cc_start: 0.5873 (mmmt) cc_final: 0.5519 (mmmt) REVERT: A 407 ARG cc_start: 0.5597 (mtt180) cc_final: 0.5282 (mtt90) REVERT: A 448 ASN cc_start: 0.7694 (t0) cc_final: 0.7161 (p0) REVERT: A 596 TYR cc_start: 0.3390 (m-80) cc_final: 0.3155 (m-80) REVERT: A 614 ILE cc_start: 0.5517 (mp) cc_final: 0.5002 (mp) REVERT: A 640 MET cc_start: -0.0502 (OUTLIER) cc_final: -0.0907 (ppp) REVERT: A 656 MET cc_start: 0.0001 (mmp) cc_final: -0.0864 (mmp) REVERT: A 800 MET cc_start: 0.4013 (ttt) cc_final: 0.3552 (ppp) REVERT: A 815 SER cc_start: 0.7724 (m) cc_final: 0.7505 (m) REVERT: A 842 MET cc_start: 0.0846 (mmp) cc_final: 0.0464 (tpt) REVERT: A 859 MET cc_start: 0.6913 (tpp) cc_final: 0.6451 (tmm) REVERT: A 891 MET cc_start: -0.1086 (ptt) cc_final: -0.1402 (ptt) REVERT: A 996 MET cc_start: 0.0482 (ttm) cc_final: -0.1344 (mmt) outliers start: 140 outliers final: 94 residues processed: 337 average time/residue: 0.3700 time to fit residues: 196.8526 Evaluate side-chains 300 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 194 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 381 ASN Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 181 HIS Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 853 MET Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 470 TRP Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 167 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 110 optimal weight: 30.0000 chunk 81 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 161 optimal weight: 0.0370 chunk 12 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 275 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 146 GLN F 208 GLN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.180595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.144165 restraints weight = 82867.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.142877 restraints weight = 51828.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.142421 restraints weight = 41052.204| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.7326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25230 Z= 0.136 Angle : 0.688 11.798 34078 Z= 0.358 Chirality : 0.046 0.212 3796 Planarity : 0.004 0.048 4332 Dihedral : 6.488 93.705 3372 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.10 % Favored : 92.44 % Rotamer: Outliers : 4.00 % Allowed : 27.59 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.15), residues: 3002 helix: -0.24 (0.15), residues: 1068 sheet: -0.72 (0.23), residues: 516 loop : -2.20 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 43 HIS 0.004 0.001 HIS C 252 PHE 0.028 0.002 PHE F 188 TYR 0.025 0.002 TYR A 741 ARG 0.009 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 884) hydrogen bonds : angle 5.29335 ( 2520) covalent geometry : bond 0.00302 (25230) covalent geometry : angle 0.68792 (34078) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 206 time to evaluate : 2.691 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: F 1 MET cc_start: 0.0162 (tpp) cc_final: -0.1482 (tmm) REVERT: F 138 MET cc_start: 0.7248 (ttm) cc_final: 0.6847 (mpp) REVERT: F 367 ASP cc_start: 0.7544 (p0) cc_final: 0.7220 (p0) REVERT: F 373 ASN cc_start: 0.8465 (m-40) cc_final: 0.7947 (m-40) REVERT: F 375 MET cc_start: 0.7263 (mmm) cc_final: 0.6983 (mmm) REVERT: F 390 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8394 (mm-30) REVERT: E 23 MET cc_start: 0.1686 (ttp) cc_final: 0.1175 (ttm) REVERT: E 57 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6619 (mt) REVERT: E 167 ARG cc_start: 0.7518 (tpt170) cc_final: 0.7261 (mmm160) REVERT: E 177 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7810 (mp) REVERT: E 181 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.7180 (t-170) REVERT: D 60 MET cc_start: 0.7886 (mpp) cc_final: 0.7414 (mpp) REVERT: D 70 GLU cc_start: 0.5689 (mt-10) cc_final: 0.5381 (mt-10) REVERT: D 303 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8071 (p0) REVERT: D 357 MET cc_start: 0.8326 (tpp) cc_final: 0.8124 (tpp) REVERT: D 486 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7484 (m-10) REVERT: D 492 MET cc_start: 0.8343 (mmt) cc_final: 0.7889 (mmt) REVERT: D 611 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.5705 (mt-10) REVERT: D 800 MET cc_start: 0.6458 (tpt) cc_final: 0.6033 (tpt) REVERT: D 806 TYR cc_start: 0.7436 (m-80) cc_final: 0.6935 (m-80) REVERT: D 828 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.7141 (m) REVERT: D 853 MET cc_start: 0.5939 (OUTLIER) cc_final: 0.5623 (tpp) REVERT: D 858 ARG cc_start: -0.1025 (OUTLIER) cc_final: -0.3606 (ptp-170) REVERT: D 859 MET cc_start: 0.6658 (tpp) cc_final: 0.6394 (tpp) REVERT: D 891 MET cc_start: 0.3945 (tpp) cc_final: 0.3717 (tpp) REVERT: D 960 LEU cc_start: 0.1845 (OUTLIER) cc_final: 0.1526 (pp) REVERT: C 1 MET cc_start: 0.4869 (tmm) cc_final: 0.4497 (tmm) REVERT: C 25 SER cc_start: 0.7384 (t) cc_final: 0.6204 (p) REVERT: C 29 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5957 (tp30) REVERT: C 339 ASN cc_start: 0.6429 (t0) cc_final: 0.5610 (m-40) REVERT: C 376 ARG cc_start: 0.4260 (mmt180) cc_final: 0.2441 (tpt170) REVERT: C 414 PHE cc_start: 0.5486 (OUTLIER) cc_final: 0.5037 (m-80) REVERT: B 23 MET cc_start: 0.3856 (ppp) cc_final: 0.2928 (ptp) REVERT: B 158 LEU cc_start: 0.5331 (OUTLIER) cc_final: 0.4878 (mm) REVERT: A 158 ILE cc_start: -0.3251 (OUTLIER) cc_final: -0.3458 (pt) REVERT: A 230 MET cc_start: -0.2441 (ttp) cc_final: -0.3045 (ttm) REVERT: A 298 CYS cc_start: 0.5077 (m) cc_final: 0.4824 (p) REVERT: A 351 LYS cc_start: 0.5691 (mmmt) cc_final: 0.5349 (mmmt) REVERT: A 448 ASN cc_start: 0.7594 (t0) cc_final: 0.7085 (p0) REVERT: A 640 MET cc_start: -0.0397 (OUTLIER) cc_final: -0.0876 (ppp) REVERT: A 656 MET cc_start: -0.0649 (mmp) cc_final: -0.1258 (mmp) REVERT: A 800 MET cc_start: 0.3962 (ttt) cc_final: 0.3601 (ppp) REVERT: A 815 SER cc_start: 0.7736 (m) cc_final: 0.7501 (m) REVERT: A 842 MET cc_start: 0.0790 (mmp) cc_final: 0.0417 (tpt) REVERT: A 859 MET cc_start: 0.6742 (tpp) cc_final: 0.6202 (tmm) REVERT: A 891 MET cc_start: -0.0783 (ptt) cc_final: -0.1040 (ptt) REVERT: A 996 MET cc_start: 0.0810 (ttm) cc_final: -0.1093 (mmt) outliers start: 112 outliers final: 83 residues processed: 309 average time/residue: 0.3682 time to fit residues: 178.2854 Evaluate side-chains 287 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 189 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 181 HIS Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 815 SER Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 853 MET Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 470 TRP Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 964 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 90 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 289 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 214 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 231 ASN ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 785 ASN ** 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 = 0.4888 r_free = 0.4888 target = 0.178690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.140782 restraints weight = 83293.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.139311 restraints weight = 55368.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.139879 restraints weight = 38892.971| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.7650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25230 Z= 0.178 Angle : 0.726 11.268 34078 Z= 0.380 Chirality : 0.047 0.262 3796 Planarity : 0.005 0.061 4332 Dihedral : 6.555 92.994 3372 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.36 % Favored : 91.17 % Rotamer: Outliers : 3.82 % Allowed : 28.06 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.15), residues: 3002 helix: -0.37 (0.15), residues: 1078 sheet: -0.77 (0.23), residues: 520 loop : -2.23 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 470 HIS 0.005 0.001 HIS E 16 PHE 0.029 0.002 PHE F 188 TYR 0.043 0.002 TYR A 741 ARG 0.011 0.001 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 884) hydrogen bonds : angle 5.38130 ( 2520) covalent geometry : bond 0.00406 (25230) covalent geometry : angle 0.72590 (34078) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 203 time to evaluate : 2.687 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: F 1 MET cc_start: 0.0023 (tpp) cc_final: -0.1495 (tmm) REVERT: F 138 MET cc_start: 0.7231 (ttm) cc_final: 0.6727 (mpp) REVERT: F 257 LYS cc_start: 0.6469 (pttt) cc_final: 0.6110 (pttp) REVERT: F 367 ASP cc_start: 0.7548 (p0) cc_final: 0.7224 (p0) REVERT: F 373 ASN cc_start: 0.8516 (m-40) cc_final: 0.8034 (m-40) REVERT: F 375 MET cc_start: 0.7173 (mmm) cc_final: 0.6909 (mmm) REVERT: F 390 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8437 (mm-30) REVERT: E 23 MET cc_start: 0.1833 (ttp) cc_final: 0.1458 (ttm) REVERT: E 167 ARG cc_start: 0.7736 (tpt170) cc_final: 0.7075 (tpt90) REVERT: E 177 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7906 (mp) REVERT: E 181 HIS cc_start: 0.7514 (OUTLIER) cc_final: 0.7231 (t70) REVERT: D 60 MET cc_start: 0.7913 (mpp) cc_final: 0.7421 (mpp) REVERT: D 70 GLU cc_start: 0.6150 (mt-10) cc_final: 0.5737 (mt-10) REVERT: D 357 MET cc_start: 0.8384 (tpp) cc_final: 0.8167 (tpp) REVERT: D 492 MET cc_start: 0.8328 (mmt) cc_final: 0.7920 (mmt) REVERT: D 611 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.5626 (tt0) REVERT: D 800 MET cc_start: 0.6401 (tpt) cc_final: 0.5993 (tpt) REVERT: D 806 TYR cc_start: 0.7490 (m-80) cc_final: 0.7050 (m-80) REVERT: D 828 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.6970 (m) REVERT: D 853 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5635 (tpp) REVERT: D 858 ARG cc_start: -0.0126 (OUTLIER) cc_final: -0.3042 (ptp-170) REVERT: D 960 LEU cc_start: 0.1945 (OUTLIER) cc_final: 0.1645 (pp) REVERT: C 25 SER cc_start: 0.7615 (t) cc_final: 0.6532 (p) REVERT: C 29 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5936 (tp30) REVERT: C 339 ASN cc_start: 0.6327 (t0) cc_final: 0.5451 (m-40) REVERT: C 376 ARG cc_start: 0.4143 (mmt180) cc_final: 0.2297 (tpt170) REVERT: C 414 PHE cc_start: 0.5501 (OUTLIER) cc_final: 0.5053 (m-80) REVERT: B 23 MET cc_start: 0.4102 (ppp) cc_final: 0.3212 (ptp) REVERT: B 158 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.4979 (mm) REVERT: A 230 MET cc_start: -0.2197 (ttp) cc_final: -0.2793 (ttm) REVERT: A 298 CYS cc_start: 0.5003 (m) cc_final: 0.4670 (p) REVERT: A 351 LYS cc_start: 0.5736 (mmmt) cc_final: 0.5409 (mmmt) REVERT: A 448 ASN cc_start: 0.7878 (t0) cc_final: 0.7420 (p0) REVERT: A 490 GLN cc_start: 0.4838 (pm20) cc_final: 0.4493 (pm20) REVERT: A 640 MET cc_start: -0.0557 (OUTLIER) cc_final: -0.0993 (ppp) REVERT: A 656 MET cc_start: -0.0267 (mmp) cc_final: -0.0951 (mmp) REVERT: A 671 MET cc_start: 0.8113 (pmm) cc_final: 0.7674 (pmm) REVERT: A 800 MET cc_start: 0.3680 (ttt) cc_final: 0.3152 (ppp) REVERT: A 815 SER cc_start: 0.7648 (m) cc_final: 0.7442 (m) REVERT: A 842 MET cc_start: 0.0823 (mmp) cc_final: 0.0472 (tpt) REVERT: A 859 MET cc_start: 0.6634 (tpp) cc_final: 0.6137 (tmm) REVERT: A 996 MET cc_start: 0.0818 (ttm) cc_final: -0.0809 (mmt) outliers start: 107 outliers final: 87 residues processed: 303 average time/residue: 0.3558 time to fit residues: 171.6055 Evaluate side-chains 290 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 192 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 181 HIS Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 815 SER Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 837 LYS Chi-restraints excluded: chain D residue 853 MET Chi-restraints excluded: chain D residue 858 ARG Chi-restraints excluded: chain D residue 932 TYR Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 470 TRP Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 960 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 154 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 273 optimal weight: 0.0970 chunk 242 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS ** A 785 ASN ** 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 = 0.4888 r_free = 0.4888 target = 0.178743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.141250 restraints weight = 83293.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.139338 restraints weight = 54380.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.139913 restraints weight = 42152.191| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.7668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 25230 Z= 0.227 Angle : 0.840 59.124 34078 Z= 0.467 Chirality : 0.049 1.018 3796 Planarity : 0.005 0.081 4332 Dihedral : 6.577 92.965 3372 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.33 % Favored : 91.17 % Rotamer: Outliers : 4.00 % Allowed : 27.91 % Favored : 68.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.15), residues: 3002 helix: -0.39 (0.15), residues: 1078 sheet: -0.76 (0.23), residues: 520 loop : -2.23 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 470 HIS 0.004 0.001 HIS E 16 PHE 0.061 0.002 PHE A 743 TYR 0.112 0.002 TYR A 741 ARG 0.045 0.001 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 884) hydrogen bonds : angle 5.40782 ( 2520) covalent geometry : bond 0.00509 (25230) covalent geometry : angle 0.84039 (34078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12011.49 seconds wall clock time: 211 minutes 20.73 seconds (12680.73 seconds total)