Starting phenix.real_space_refine on Mon Aug 25 02:18:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hlz_34886/08_2025/8hlz_34886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hlz_34886/08_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_34886/08_2025/8hlz_34886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hlz_34886/08_2025/8hlz_34886.map" model { file = "/net/cci-nas-00/data/ceres_data/8hlz_34886/08_2025/8hlz_34886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hlz_34886/08_2025/8hlz_34886.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.99, per 1000 atoms: 0.24 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: 2.09 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.08 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: 5.08 Time building geometry restraints manager: 2.86 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.120 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.950 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.029 0.002 ARG B 61 TYR 0.028 0.003 TYR A 140 PHE 0.045 0.003 PHE C 215 TRP 0.024 0.003 TRP A 470 HIS 0.008 0.002 HIS D 461 Details of bonding type rmsd covalent geometry : bond 0.00959 (25230) covalent geometry : angle 1.14835 (34078) hydrogen bonds : bond 0.17783 ( 884) hydrogen bonds : angle 8.03541 ( 2520) *********************** 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 : 0.962 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: 0.1927 time to fit residues: 319.3300 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 : 1.082 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 105 GLN F 351 GLN ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS D 141 HIS D 147 ASN ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN D 225 GLN D 274 ASN D 562 ASN D 585 GLN D 600 HIS ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 ASN D 937 ASN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.185867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.147845 restraints weight = 84891.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.146174 restraints weight = 44468.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.147202 restraints weight = 33088.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.147225 restraints weight = 27662.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.147222 restraints weight = 26694.768| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 25230 Z= 0.221 Angle : 0.848 12.082 34078 Z= 0.447 Chirality : 0.051 0.278 3796 Planarity : 0.006 0.080 4332 Dihedral : 11.417 102.651 3621 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.09 % Favored : 91.27 % Rotamer: Outliers : 9.15 % Allowed : 23.55 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.14), residues: 3002 helix: -1.60 (0.14), residues: 1080 sheet: -1.41 (0.23), residues: 500 loop : -2.81 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG A 234 TYR 0.028 0.002 TYR A 681 PHE 0.024 0.003 PHE F 152 TRP 0.038 0.003 TRP D 470 HIS 0.006 0.001 HIS D 185 Details of bonding type rmsd covalent geometry : bond 0.00490 (25230) covalent geometry : angle 0.84785 (34078) hydrogen bonds : bond 0.05535 ( 884) hydrogen bonds : angle 6.10868 ( 2520) *********************** 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 554 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 298 time to evaluate : 1.120 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: F 1 MET cc_start: 0.0042 (tpp) cc_final: -0.0159 (tpp) REVERT: F 246 LEU cc_start: 0.6966 (mt) cc_final: 0.6294 (tp) REVERT: F 260 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.5820 (pp20) REVERT: F 275 LEU cc_start: 0.7805 (tp) cc_final: 0.6881 (pp) REVERT: F 291 LYS cc_start: 0.8458 (pptt) cc_final: 0.8201 (tppt) REVERT: F 294 ILE cc_start: 0.6272 (mm) cc_final: 0.5960 (mm) REVERT: F 351 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: F 380 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: E 142 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7394 (mmmt) REVERT: E 167 ARG cc_start: 0.7127 (tpt170) cc_final: 0.6739 (mmm160) REVERT: E 181 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6690 (t-170) REVERT: D 187 SER cc_start: 0.5966 (OUTLIER) cc_final: 0.5481 (m) REVERT: D 207 MET cc_start: 0.5756 (ttt) cc_final: 0.5469 (mtp) REVERT: D 369 THR cc_start: 0.6569 (OUTLIER) cc_final: 0.6331 (t) REVERT: D 656 MET cc_start: 0.8625 (mmm) cc_final: 0.7910 (mmt) REVERT: D 711 MET cc_start: 0.4734 (tmm) cc_final: 0.4333 (tmm) REVERT: D 716 ASN cc_start: 0.6321 (OUTLIER) cc_final: 0.6049 (p0) REVERT: D 765 ASP cc_start: 0.4840 (OUTLIER) cc_final: 0.4592 (t0) REVERT: D 809 MET cc_start: 0.6443 (mmm) cc_final: 0.6232 (mmm) REVERT: D 828 THR cc_start: 0.7487 (OUTLIER) cc_final: 0.6544 (m) REVERT: D 853 MET cc_start: 0.5414 (OUTLIER) cc_final: 0.4840 (tpp) REVERT: D 858 ARG cc_start: -0.1260 (OUTLIER) cc_final: -0.2854 (ptp90) REVERT: D 891 MET cc_start: 0.4980 (mpp) cc_final: 0.4748 (mpp) REVERT: D 932 TYR cc_start: 0.5367 (OUTLIER) cc_final: 0.4673 (m-80) REVERT: C 29 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5862 (tp30) REVERT: C 183 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7518 (pp) REVERT: C 339 ASN cc_start: 0.6896 (t0) cc_final: 0.6206 (m-40) REVERT: C 376 ARG cc_start: 0.3861 (mmt180) cc_final: 0.2256 (tpt-90) REVERT: C 390 GLU cc_start: 0.4993 (OUTLIER) cc_final: 0.4645 (mp0) REVERT: B 1 MET cc_start: 0.7303 (mmp) cc_final: 0.6511 (tpp) REVERT: B 23 MET cc_start: 0.2797 (ppp) cc_final: 0.2286 (ptp) REVERT: B 178 VAL cc_start: 0.0785 (OUTLIER) cc_final: 0.0570 (p) REVERT: A 210 GLU cc_start: 0.5157 (OUTLIER) cc_final: 0.4800 (tp30) REVERT: A 223 ARG cc_start: 0.2949 (OUTLIER) cc_final: 0.0769 (mmt90) REVERT: A 332 TYR cc_start: 0.7252 (t80) cc_final: 0.6960 (t80) REVERT: A 356 CYS cc_start: 0.2479 (OUTLIER) cc_final: 0.1444 (p) REVERT: A 368 MET cc_start: 0.0143 (mtp) cc_final: -0.0310 (mmt) REVERT: A 428 ILE cc_start: 0.2189 (OUTLIER) cc_final: 0.1905 (mp) REVERT: A 511 LEU cc_start: -0.0964 (OUTLIER) cc_final: -0.1176 (mm) REVERT: A 698 LEU cc_start: 0.7520 (tp) cc_final: 0.7076 (pp) REVERT: A 764 VAL cc_start: 0.1928 (p) cc_final: 0.1416 (p) REVERT: A 819 SER cc_start: 0.2602 (OUTLIER) cc_final: 0.1793 (p) REVERT: A 837 LYS cc_start: -0.5975 (OUTLIER) cc_final: -0.6437 (mttt) REVERT: A 842 MET cc_start: 0.1311 (mmp) cc_final: 0.0678 (tpt) REVERT: A 859 MET cc_start: 0.6717 (tpp) cc_final: 0.5545 (tmm) outliers start: 256 outliers final: 133 residues processed: 522 average time/residue: 0.1813 time to fit residues: 148.4264 Evaluate side-chains 391 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 235 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 105 GLN 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 215 PHE 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 348 ILE Chi-restraints excluded: chain F residue 351 GLN 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 F residue 409 GLN Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 GLU 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 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 203 GLU 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 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 240 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 271 TYR 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 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 470 TRP Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 551 ASN 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 645 THR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 716 ASN 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 765 ASP Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 786 ASN Chi-restraints excluded: chain D residue 797 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 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 24 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 258 VAL 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 C residue 412 SER 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 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 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 177 SER 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 229 GLU 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 376 THR 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 572 VAL 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 759 ILE Chi-restraints excluded: chain A residue 809 MET 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 204 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 253 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 294 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 chunk 176 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN F 381 ASN ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN D 352 ASN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 ASN ** D 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 985 ASN C 397 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 HIS ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 963 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.179350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.140991 restraints weight = 85937.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.140428 restraints weight = 53521.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.140285 restraints weight = 37637.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.140709 restraints weight = 34379.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.140896 restraints weight = 29432.946| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 25230 Z= 0.297 Angle : 0.868 12.729 34078 Z= 0.460 Chirality : 0.052 0.254 3796 Planarity : 0.006 0.066 4332 Dihedral : 9.633 97.323 3463 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.49 % Favored : 89.87 % Rotamer: Outliers : 8.54 % Allowed : 24.55 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.14), residues: 3002 helix: -1.45 (0.14), residues: 1084 sheet: -1.25 (0.23), residues: 482 loop : -2.70 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 727 TYR 0.041 0.003 TYR E 15 PHE 0.031 0.003 PHE F 152 TRP 0.049 0.003 TRP D 470 HIS 0.028 0.003 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00674 (25230) covalent geometry : angle 0.86808 (34078) hydrogen bonds : bond 0.05573 ( 884) hydrogen bonds : angle 6.04740 ( 2520) *********************** 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 478 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 239 time to evaluate : 0.994 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: F 260 GLU cc_start: 0.5609 (OUTLIER) cc_final: 0.5074 (pp20) REVERT: F 323 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7453 (mt) REVERT: F 390 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7940 (mp0) REVERT: F 393 ASN cc_start: 0.8876 (m-40) cc_final: 0.8667 (m-40) REVERT: E 15 TYR cc_start: 0.5245 (m-10) cc_final: 0.4929 (m-10) REVERT: E 109 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6575 (p0) REVERT: E 142 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7543 (mmmt) REVERT: E 177 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7131 (mp) REVERT: E 181 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.6833 (t-90) REVERT: D 357 MET cc_start: 0.8676 (mmm) cc_final: 0.8409 (tpp) REVERT: D 369 THR cc_start: 0.6632 (OUTLIER) cc_final: 0.6378 (t) REVERT: D 492 MET cc_start: 0.8349 (mmt) cc_final: 0.8048 (mmt) REVERT: D 611 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6339 (tt0) REVERT: D 641 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6401 (tt) REVERT: D 656 MET cc_start: 0.8756 (mmm) cc_final: 0.8519 (mmt) REVERT: D 657 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7863 (pt0) REVERT: D 711 MET cc_start: 0.5006 (tmm) cc_final: 0.4775 (tmm) REVERT: D 716 ASN cc_start: 0.6410 (OUTLIER) cc_final: 0.6026 (p0) REVERT: D 724 MET cc_start: 0.7785 (tpt) cc_final: 0.7463 (tmm) REVERT: D 726 ASP cc_start: 0.6973 (m-30) cc_final: 0.6736 (m-30) REVERT: D 743 PHE cc_start: 0.6119 (m-10) cc_final: 0.5873 (m-10) REVERT: D 765 ASP cc_start: 0.6075 (OUTLIER) cc_final: 0.5638 (t0) REVERT: D 809 MET cc_start: 0.6853 (mmm) cc_final: 0.6557 (mmm) REVERT: D 828 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.6794 (m) REVERT: D 829 SER cc_start: 0.2095 (OUTLIER) cc_final: 0.1675 (m) REVERT: D 853 MET cc_start: 0.5556 (ttp) cc_final: 0.4744 (tpp) REVERT: D 858 ARG cc_start: -0.0977 (OUTLIER) cc_final: -0.3238 (ptp90) REVERT: D 932 TYR cc_start: 0.5468 (OUTLIER) cc_final: 0.4861 (m-80) REVERT: C 18 LYS cc_start: 0.6616 (OUTLIER) cc_final: 0.6393 (pttm) REVERT: C 29 GLU cc_start: 0.5791 (OUTLIER) cc_final: 0.5412 (tp30) REVERT: C 183 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7493 (pp) REVERT: C 255 ARG cc_start: 0.6317 (OUTLIER) cc_final: 0.5882 (ptm-80) REVERT: C 257 LYS cc_start: 0.7667 (tppt) cc_final: 0.7395 (tmmt) REVERT: C 295 ASP cc_start: 0.4516 (m-30) cc_final: 0.4294 (p0) REVERT: C 339 ASN cc_start: 0.6375 (t0) cc_final: 0.5577 (m-40) REVERT: C 376 ARG cc_start: 0.4103 (mmt180) cc_final: 0.2425 (tpt170) REVERT: C 390 GLU cc_start: 0.4929 (OUTLIER) cc_final: 0.4655 (mp0) REVERT: B 23 MET cc_start: 0.2759 (ppp) cc_final: 0.2378 (ptp) REVERT: B 41 GLU cc_start: 0.7697 (pp20) cc_final: 0.7078 (pp20) REVERT: B 57 LEU cc_start: 0.6809 (mt) cc_final: 0.6472 (mt) REVERT: A 34 PHE cc_start: 0.2338 (OUTLIER) cc_final: 0.1623 (t80) REVERT: A 148 CYS cc_start: 0.5190 (t) cc_final: 0.4748 (m) REVERT: A 158 ILE cc_start: -0.2275 (OUTLIER) cc_final: -0.2903 (pt) REVERT: A 210 GLU cc_start: 0.4328 (OUTLIER) cc_final: 0.3976 (tp30) REVERT: A 223 ARG cc_start: 0.2520 (OUTLIER) cc_final: 0.0220 (mmt90) REVERT: A 230 MET cc_start: -0.2070 (ttp) cc_final: -0.2870 (ttm) REVERT: A 298 CYS cc_start: 0.5203 (p) cc_final: 0.4924 (m) REVERT: A 368 MET cc_start: 0.0608 (mtp) cc_final: -0.0172 (mmt) REVERT: A 428 ILE cc_start: 0.2319 (OUTLIER) cc_final: 0.2059 (mp) REVERT: A 698 LEU cc_start: 0.7904 (tp) cc_final: 0.7522 (pp) REVERT: A 837 LYS cc_start: -0.5861 (OUTLIER) cc_final: -0.6254 (mptt) REVERT: A 842 MET cc_start: 0.1363 (mmp) cc_final: 0.0601 (tpt) REVERT: A 853 MET cc_start: 0.0692 (OUTLIER) cc_final: -0.0136 (mmp) REVERT: A 859 MET cc_start: 0.6817 (tpp) cc_final: 0.5624 (tmm) REVERT: A 891 MET cc_start: 0.2234 (OUTLIER) cc_final: 0.1884 (mmm) REVERT: A 892 LEU cc_start: 0.0898 (OUTLIER) cc_final: 0.0547 (tt) outliers start: 239 outliers final: 140 residues processed: 449 average time/residue: 0.1850 time to fit residues: 129.0912 Evaluate side-chains 371 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 202 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 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 251 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 261 HIS Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 348 ILE 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 409 GLN Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain E residue 37 LEU 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 88 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 166 ILE 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 208 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 34 PHE 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 110 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 280 THR 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 369 THR 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 406 ILE 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 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 608 LEU Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 716 ASN 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 744 ARG Chi-restraints excluded: chain D residue 746 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 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 980 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 18 LYS 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 183 ILE Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 412 SER 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 117 ILE Chi-restraints excluded: chain B residue 130 THR 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 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 34 PHE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 142 CYS 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 229 GLU Chi-restraints excluded: chain A residue 237 VAL 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 399 GLU 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 511 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 608 LEU 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 759 ILE Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 815 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 853 MET 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 Chi-restraints excluded: chain A residue 964 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 145 optimal weight: 7.9990 chunk 68 optimal weight: 0.1980 chunk 247 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 266 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 GLN ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 ASN ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 ASN D 141 HIS ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 HIS ** 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 146 GLN A 56 ASN A 204 ASN A 336 GLN ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.181163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.144444 restraints weight = 85560.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.142022 restraints weight = 52868.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.143086 restraints weight = 40370.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.143436 restraints weight = 32191.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.143543 restraints weight = 28252.591| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25230 Z= 0.157 Angle : 0.703 12.585 34078 Z= 0.370 Chirality : 0.047 0.244 3796 Planarity : 0.005 0.058 4332 Dihedral : 8.453 92.577 3436 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.40 % Favored : 92.07 % Rotamer: Outliers : 6.79 % Allowed : 25.77 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.14), residues: 3002 helix: -0.98 (0.15), residues: 1086 sheet: -1.27 (0.23), residues: 510 loop : -2.48 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 286 TYR 0.020 0.002 TYR F 199 PHE 0.025 0.002 PHE F 152 TRP 0.030 0.002 TRP D 470 HIS 0.010 0.001 HIS D 600 Details of bonding type rmsd covalent geometry : bond 0.00343 (25230) covalent geometry : angle 0.70314 (34078) hydrogen bonds : bond 0.04346 ( 884) hydrogen bonds : angle 5.58718 ( 2520) *********************** 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 425 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 235 time to evaluate : 1.028 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: F 129 PHE cc_start: 0.5899 (OUTLIER) cc_final: 0.5595 (m-80) REVERT: F 306 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7461 (mtmm) REVERT: F 390 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8455 (mm-30) REVERT: F 393 ASN cc_start: 0.8911 (m-40) cc_final: 0.8696 (m-40) REVERT: E 1 MET cc_start: 0.4083 (tpt) cc_final: 0.3768 (tpt) REVERT: E 109 ASN cc_start: 0.6965 (OUTLIER) cc_final: 0.6214 (p0) REVERT: E 193 ARG cc_start: 0.2918 (mtm110) cc_final: 0.2718 (mtm180) REVERT: D 369 THR cc_start: 0.7143 (OUTLIER) cc_final: 0.6905 (t) REVERT: D 486 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7899 (m-10) REVERT: D 605 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7076 (tt) REVERT: D 611 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5704 (mt-10) REVERT: D 656 MET cc_start: 0.8388 (mmm) cc_final: 0.7486 (mmt) REVERT: D 711 MET cc_start: 0.5021 (tmm) cc_final: 0.4819 (tmm) REVERT: D 716 ASN cc_start: 0.6593 (OUTLIER) cc_final: 0.6166 (p0) REVERT: D 765 ASP cc_start: 0.6075 (OUTLIER) cc_final: 0.5830 (t0) REVERT: D 798 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7792 (tt) REVERT: D 808 THR cc_start: 0.6984 (p) cc_final: 0.6407 (p) REVERT: D 809 MET cc_start: 0.6982 (mmm) cc_final: 0.6680 (mmm) REVERT: D 828 THR cc_start: 0.7262 (OUTLIER) cc_final: 0.6901 (m) REVERT: D 853 MET cc_start: 0.5545 (ttp) cc_final: 0.4623 (tpp) REVERT: D 858 ARG cc_start: -0.0893 (OUTLIER) cc_final: -0.3216 (ptp90) REVERT: D 859 MET cc_start: 0.7050 (tpp) cc_final: 0.6781 (tpp) REVERT: C 29 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5562 (tp30) REVERT: C 122 ASN cc_start: 0.5150 (m-40) cc_final: 0.4615 (p0) REVERT: C 177 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: C 257 LYS cc_start: 0.7585 (tppt) cc_final: 0.7213 (tmmt) REVERT: C 339 ASN cc_start: 0.6184 (t0) cc_final: 0.5457 (m-40) REVERT: C 376 ARG cc_start: 0.4185 (mmt180) cc_final: 0.2290 (tpt170) REVERT: C 390 GLU cc_start: 0.4766 (OUTLIER) cc_final: 0.4400 (mm-30) REVERT: C 414 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.5403 (m-80) REVERT: B 23 MET cc_start: 0.2817 (ppp) cc_final: 0.2376 (ptp) REVERT: A 148 CYS cc_start: 0.5363 (t) cc_final: 0.4695 (m) REVERT: A 158 ILE cc_start: -0.1943 (OUTLIER) cc_final: -0.2599 (pt) REVERT: A 210 GLU cc_start: 0.4874 (OUTLIER) cc_final: 0.4499 (tp30) REVERT: A 223 ARG cc_start: 0.2951 (OUTLIER) cc_final: 0.0868 (mmt90) REVERT: A 230 MET cc_start: -0.2160 (ttp) cc_final: -0.2822 (ttm) REVERT: A 368 MET cc_start: 0.0548 (mtp) cc_final: -0.0301 (mmm) REVERT: A 614 ILE cc_start: 0.5870 (mp) cc_final: 0.5544 (mp) REVERT: A 698 LEU cc_start: 0.7899 (tp) cc_final: 0.7587 (pp) REVERT: A 842 MET cc_start: 0.0940 (mmp) cc_final: 0.0501 (tpt) REVERT: A 859 MET cc_start: 0.6688 (tpp) cc_final: 0.5948 (tmm) REVERT: A 892 LEU cc_start: 0.1036 (OUTLIER) cc_final: 0.0826 (tt) outliers start: 190 outliers final: 127 residues processed: 400 average time/residue: 0.1750 time to fit residues: 111.0513 Evaluate side-chains 359 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 212 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 168 ILE 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 264 VAL Chi-restraints excluded: chain F residue 306 LYS 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 E residue 37 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 88 SER 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 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 178 VAL 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 211 ASN Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain D residue 75 ASN 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 178 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 251 LEU 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 369 THR 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 407 ARG 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 486 TYR Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 572 VAL 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 636 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 716 ASN 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 744 ARG Chi-restraints excluded: chain D residue 746 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 798 LEU 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 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 177 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 352 SER 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 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 130 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 201 LEU 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 19 TYR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 142 CYS 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 229 GLU 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 399 GLU Chi-restraints excluded: chain A residue 413 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 608 LEU 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 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 853 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 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 299 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 ASN F 208 GLN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 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 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A 225 GLN ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.176886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.138819 restraints weight = 86048.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.136631 restraints weight = 45918.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.137549 restraints weight = 37726.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.137472 restraints weight = 29320.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.137622 restraints weight = 28522.228| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 25230 Z= 0.261 Angle : 0.803 11.554 34078 Z= 0.425 Chirality : 0.050 0.249 3796 Planarity : 0.006 0.057 4332 Dihedral : 8.093 92.924 3406 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.33 % Favored : 90.14 % Rotamer: Outliers : 7.90 % Allowed : 25.45 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.14), residues: 3002 helix: -1.17 (0.14), residues: 1086 sheet: -1.31 (0.24), residues: 468 loop : -2.48 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 61 TYR 0.049 0.003 TYR A 637 PHE 0.031 0.002 PHE F 152 TRP 0.047 0.003 TRP D 470 HIS 0.007 0.002 HIS D 36 Details of bonding type rmsd covalent geometry : bond 0.00592 (25230) covalent geometry : angle 0.80279 (34078) hydrogen bonds : bond 0.04973 ( 884) hydrogen bonds : angle 5.83482 ( 2520) *********************** 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 434 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 213 time to evaluate : 1.011 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: -0.0104 (tpp) cc_final: -0.1515 (tmm) REVERT: F 129 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.5505 (m-80) REVERT: F 216 SER cc_start: 0.1276 (OUTLIER) cc_final: 0.1052 (m) REVERT: F 306 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7466 (mtmm) REVERT: F 375 MET cc_start: 0.7114 (mmm) cc_final: 0.6674 (mmm) REVERT: F 380 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7638 (mm-30) REVERT: F 390 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8304 (mm-30) REVERT: F 393 ASN cc_start: 0.8928 (m-40) cc_final: 0.8728 (m-40) REVERT: E 109 ASN cc_start: 0.7225 (OUTLIER) cc_final: 0.6645 (p0) REVERT: E 181 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.7008 (t70) REVERT: D 47 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8030 (t80) REVERT: D 82 LYS cc_start: 0.7708 (mmmt) cc_final: 0.7492 (mmmt) REVERT: D 303 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7998 (p0) REVERT: D 357 MET cc_start: 0.8718 (tpp) cc_final: 0.8377 (mmp) REVERT: D 369 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6905 (t) REVERT: D 492 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8035 (mtt) REVERT: D 605 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7180 (tt) REVERT: D 611 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6035 (tt0) REVERT: D 714 PHE cc_start: 0.7516 (m-10) cc_final: 0.7309 (m-10) REVERT: D 716 ASN cc_start: 0.6662 (OUTLIER) cc_final: 0.6305 (p0) REVERT: D 798 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7832 (tt) REVERT: D 808 THR cc_start: 0.6892 (p) cc_final: 0.6312 (p) REVERT: D 809 MET cc_start: 0.6958 (mmm) cc_final: 0.6657 (mmm) REVERT: D 828 THR cc_start: 0.6979 (OUTLIER) cc_final: 0.6742 (p) REVERT: D 853 MET cc_start: 0.6023 (ttp) cc_final: 0.5137 (tpp) REVERT: D 858 ARG cc_start: -0.0014 (OUTLIER) cc_final: -0.3202 (ptp90) REVERT: D 960 LEU cc_start: 0.1758 (OUTLIER) cc_final: 0.1351 (pp) REVERT: C 29 GLU cc_start: 0.5487 (OUTLIER) cc_final: 0.5126 (tp30) REVERT: C 179 GLU cc_start: 0.8249 (tp30) cc_final: 0.7931 (tp30) REVERT: C 257 LYS cc_start: 0.7579 (tppt) cc_final: 0.7244 (tmmt) REVERT: C 295 ASP cc_start: 0.4464 (m-30) cc_final: 0.4191 (p0) REVERT: C 339 ASN cc_start: 0.6187 (t0) cc_final: 0.5419 (m-40) REVERT: C 376 ARG cc_start: 0.4178 (mmt180) cc_final: 0.2324 (tpt170) REVERT: C 390 GLU cc_start: 0.4996 (OUTLIER) cc_final: 0.4297 (mm-30) REVERT: C 414 PHE cc_start: 0.5765 (OUTLIER) cc_final: 0.5294 (m-80) REVERT: B 23 MET cc_start: 0.3407 (ppp) cc_final: 0.2656 (ptp) REVERT: A 158 ILE cc_start: -0.2529 (OUTLIER) cc_final: -0.3031 (pt) REVERT: A 207 MET cc_start: -0.2681 (ttt) cc_final: -0.3007 (ttt) REVERT: A 210 GLU cc_start: 0.5185 (OUTLIER) cc_final: 0.4753 (tp30) REVERT: A 223 ARG cc_start: 0.3460 (OUTLIER) cc_final: 0.0988 (mmt90) REVERT: A 230 MET cc_start: -0.2124 (ttp) cc_final: -0.2784 (ttm) REVERT: A 298 CYS cc_start: 0.4851 (m) cc_final: 0.4584 (p) REVERT: A 368 MET cc_start: 0.0778 (mtp) cc_final: -0.0213 (mmm) REVERT: A 640 MET cc_start: -0.0430 (ptt) cc_final: -0.0972 (ppp) REVERT: A 656 MET cc_start: -0.0615 (mmp) cc_final: -0.0857 (mmp) REVERT: A 842 MET cc_start: 0.1045 (mmp) cc_final: 0.0557 (tpt) REVERT: A 859 MET cc_start: 0.6972 (tpp) cc_final: 0.6288 (tmm) outliers start: 221 outliers final: 151 residues processed: 409 average time/residue: 0.1765 time to fit residues: 113.8778 Evaluate side-chains 360 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 186 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 129 PHE 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 216 SER Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 261 HIS Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 306 LYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 87 LYS 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 146 GLN Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 181 HIS 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 E residue 217 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 48 GLN 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 108 PHE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 280 THR 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 369 THR 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 407 ARG Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 492 MET 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 569 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL 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 636 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 717 THR 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 798 LEU 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 843 ILE 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 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 247 VAL Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 352 SER 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 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 130 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR 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 50 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 142 CYS 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 229 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 506 LEU 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 598 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 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 809 MET 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 962 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 129 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 216 optimal weight: 0.0060 chunk 34 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 55 optimal weight: 0.0570 chunk 190 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.7116 ------------------------------------------------------------------------------- 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 ASN ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS A 7 ASN A 274 ASN A 296 HIS A 352 ASN A 413 ASN ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.180208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.142152 restraints weight = 83571.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.141466 restraints weight = 46616.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.141795 restraints weight = 33277.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.142123 restraints weight = 28967.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.142184 restraints weight = 25713.230| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.7072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25230 Z= 0.125 Angle : 0.676 12.154 34078 Z= 0.351 Chirality : 0.045 0.204 3796 Planarity : 0.004 0.056 4332 Dihedral : 7.283 94.890 3396 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.80 % Favored : 92.74 % Rotamer: Outliers : 5.65 % Allowed : 27.70 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.15), residues: 3002 helix: -0.59 (0.15), residues: 1082 sheet: -1.01 (0.23), residues: 490 loop : -2.32 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 186 TYR 0.037 0.002 TYR A 741 PHE 0.022 0.002 PHE F 152 TRP 0.020 0.002 TRP D 470 HIS 0.033 0.001 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00265 (25230) covalent geometry : angle 0.67573 (34078) hydrogen bonds : bond 0.03879 ( 884) hydrogen bonds : angle 5.35629 ( 2520) *********************** 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 371 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 213 time to evaluate : 0.987 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 43 TRP cc_start: 0.4015 (t-100) cc_final: 0.3686 (t-100) REVERT: F 129 PHE cc_start: 0.6334 (OUTLIER) cc_final: 0.5385 (m-80) REVERT: F 373 ASN cc_start: 0.8542 (m-40) cc_final: 0.7915 (m110) REVERT: F 375 MET cc_start: 0.6859 (mmm) cc_final: 0.6424 (mmm) REVERT: F 390 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8277 (mm-30) REVERT: E 177 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7810 (mp) REVERT: D 283 LYS cc_start: 0.4423 (OUTLIER) cc_final: 0.3876 (mtmt) REVERT: D 486 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7560 (m-10) REVERT: D 492 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7884 (mtt) REVERT: D 605 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6962 (tt) REVERT: D 611 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.5939 (tt0) REVERT: D 806 TYR cc_start: 0.7455 (m-80) cc_final: 0.7250 (m-80) REVERT: D 808 THR cc_start: 0.6585 (p) cc_final: 0.6260 (p) REVERT: D 809 MET cc_start: 0.6728 (mmm) cc_final: 0.6426 (mmm) REVERT: D 828 THR cc_start: 0.6967 (OUTLIER) cc_final: 0.6574 (m) REVERT: D 853 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.4893 (tpp) REVERT: D 858 ARG cc_start: -0.0402 (OUTLIER) cc_final: -0.3832 (ptp90) REVERT: D 891 MET cc_start: 0.3926 (mpp) cc_final: 0.3726 (tpp) REVERT: C 25 SER cc_start: 0.7379 (t) cc_final: 0.6234 (p) REVERT: C 29 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.5163 (tp30) REVERT: C 122 ASN cc_start: 0.4776 (m-40) cc_final: 0.4523 (p0) REVERT: C 177 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6689 (m-30) REVERT: C 179 GLU cc_start: 0.8102 (tp30) cc_final: 0.7663 (tp30) REVERT: C 255 ARG cc_start: 0.6132 (OUTLIER) cc_final: 0.5768 (ptm-80) REVERT: C 295 ASP cc_start: 0.4187 (m-30) cc_final: 0.3963 (p0) REVERT: C 339 ASN cc_start: 0.6091 (t0) cc_final: 0.5384 (m-40) REVERT: C 376 ARG cc_start: 0.4112 (mmt180) cc_final: 0.2517 (tpt170) REVERT: C 390 GLU cc_start: 0.4895 (OUTLIER) cc_final: 0.4687 (mp0) REVERT: C 414 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.5378 (m-80) REVERT: B 23 MET cc_start: 0.3708 (ppp) cc_final: 0.2918 (ptp) REVERT: A 158 ILE cc_start: -0.2292 (OUTLIER) cc_final: -0.2815 (pt) REVERT: A 210 GLU cc_start: 0.5081 (OUTLIER) cc_final: 0.4658 (tp30) REVERT: A 223 ARG cc_start: 0.3576 (OUTLIER) cc_final: 0.1692 (mmt90) REVERT: A 230 MET cc_start: -0.2416 (ttp) cc_final: -0.3061 (ttm) REVERT: A 298 CYS cc_start: 0.4958 (m) cc_final: 0.4655 (p) REVERT: A 368 MET cc_start: 0.0176 (mtp) cc_final: -0.0477 (mmm) REVERT: A 614 ILE cc_start: 0.5714 (mp) cc_final: 0.5355 (mp) REVERT: A 640 MET cc_start: -0.0780 (OUTLIER) cc_final: -0.1289 (ppp) REVERT: A 842 MET cc_start: 0.0752 (mmp) cc_final: 0.0326 (tpt) REVERT: A 859 MET cc_start: 0.6897 (tpp) cc_final: 0.6212 (tmm) outliers start: 158 outliers final: 96 residues processed: 352 average time/residue: 0.1728 time to fit residues: 96.1802 Evaluate side-chains 312 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 197 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 129 PHE 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 208 GLN Chi-restraints excluded: chain F residue 213 PHE 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 384 VAL Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 155 LEU 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 178 VAL 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 48 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL 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 636 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 717 THR 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 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 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 177 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 390 GLU 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 105 TYR Chi-restraints excluded: chain B residue 145 LEU 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 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 11 SER Chi-restraints excluded: chain A residue 50 LEU 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 274 ASN Chi-restraints excluded: chain A residue 338 SER 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 470 TRP 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 608 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 641 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 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 809 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 161 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 238 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 116 optimal weight: 0.0270 chunk 156 optimal weight: 10.0000 overall best weight: 1.2442 ------------------------------------------------------------------------------- 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS ** 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 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.178979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.144290 restraints weight = 85593.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.142659 restraints weight = 46250.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.143815 restraints weight = 35458.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.143345 restraints weight = 33422.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.143683 restraints weight = 29622.333| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25230 Z= 0.128 Angle : 0.674 11.365 34078 Z= 0.349 Chirality : 0.045 0.201 3796 Planarity : 0.004 0.057 4332 Dihedral : 6.562 59.750 3385 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.93 % Favored : 91.61 % Rotamer: Outliers : 4.82 % Allowed : 28.66 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.15), residues: 3002 helix: -0.45 (0.15), residues: 1082 sheet: -0.86 (0.24), residues: 492 loop : -2.25 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 286 TYR 0.050 0.001 TYR A 741 PHE 0.022 0.002 PHE D 714 TRP 0.025 0.002 TRP D 470 HIS 0.007 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00279 (25230) covalent geometry : angle 0.67374 (34078) hydrogen bonds : bond 0.03786 ( 884) hydrogen bonds : angle 5.27575 ( 2520) *********************** 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 342 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 207 time to evaluate : 0.923 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: F 43 TRP cc_start: 0.4174 (t-100) cc_final: 0.3887 (t-100) REVERT: F 129 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: F 284 GLU cc_start: 0.4163 (OUTLIER) cc_final: 0.1141 (mt-10) REVERT: F 373 ASN cc_start: 0.8409 (m-40) cc_final: 0.7932 (m-40) REVERT: F 375 MET cc_start: 0.6669 (mmm) cc_final: 0.6387 (mmm) REVERT: E 177 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7744 (mp) REVERT: D 492 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7837 (mtt) REVERT: D 605 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7064 (tt) REVERT: D 611 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6116 (tt0) REVERT: D 808 THR cc_start: 0.6290 (p) cc_final: 0.5945 (p) REVERT: D 809 MET cc_start: 0.6602 (mmm) cc_final: 0.6380 (mmm) REVERT: D 828 THR cc_start: 0.6665 (OUTLIER) cc_final: 0.6212 (m) REVERT: D 829 SER cc_start: 0.2033 (OUTLIER) cc_final: 0.1756 (m) REVERT: D 853 MET cc_start: 0.5677 (OUTLIER) cc_final: 0.4901 (tpp) REVERT: D 858 ARG cc_start: 0.0138 (OUTLIER) cc_final: -0.3126 (ptp-110) REVERT: D 960 LEU cc_start: 0.1604 (OUTLIER) cc_final: 0.1244 (pp) REVERT: D 996 MET cc_start: 0.3062 (tpt) cc_final: 0.2784 (tpt) REVERT: C 25 SER cc_start: 0.7395 (t) cc_final: 0.6177 (p) REVERT: C 29 GLU cc_start: 0.5531 (OUTLIER) cc_final: 0.5227 (tp30) REVERT: C 177 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6639 (m-30) REVERT: C 255 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5631 (ptm-80) REVERT: C 257 LYS cc_start: 0.7301 (tptt) cc_final: 0.6689 (tmtt) REVERT: C 295 ASP cc_start: 0.4221 (m-30) cc_final: 0.3982 (p0) REVERT: C 339 ASN cc_start: 0.6466 (t0) cc_final: 0.5727 (m-40) REVERT: C 376 ARG cc_start: 0.4042 (mmt180) cc_final: 0.2468 (tpt170) REVERT: C 414 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.5236 (m-80) REVERT: B 23 MET cc_start: 0.3967 (ppp) cc_final: 0.3068 (ptp) REVERT: B 158 LEU cc_start: 0.5001 (OUTLIER) cc_final: 0.4650 (mm) REVERT: A 158 ILE cc_start: -0.2493 (OUTLIER) cc_final: -0.2952 (pt) REVERT: A 230 MET cc_start: -0.2639 (ttp) cc_final: -0.3269 (ttm) REVERT: A 298 CYS cc_start: 0.4980 (m) cc_final: 0.4723 (p) REVERT: A 368 MET cc_start: 0.0330 (mtp) cc_final: -0.0424 (mmm) REVERT: A 640 MET cc_start: -0.0429 (OUTLIER) cc_final: -0.1003 (ppp) REVERT: A 707 LEU cc_start: 0.6840 (pt) cc_final: 0.6458 (tt) REVERT: A 800 MET cc_start: 0.3404 (ttt) cc_final: 0.3114 (ppp) REVERT: A 842 MET cc_start: 0.0773 (mmp) cc_final: 0.0189 (tpt) REVERT: A 859 MET cc_start: 0.6897 (tpp) cc_final: 0.6456 (tmm) outliers start: 135 outliers final: 95 residues processed: 327 average time/residue: 0.1542 time to fit residues: 81.6110 Evaluate side-chains 314 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 201 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 129 PHE 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 284 GLU 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 384 VAL Chi-restraints excluded: chain E residue 37 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 154 VAL Chi-restraints excluded: chain E residue 155 LEU 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 199 ASN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL 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 636 ARG Chi-restraints excluded: chain D residue 717 THR 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 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 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 177 ASP Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 352 SER 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 17 ASP 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 161 THR 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 50 LEU 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 274 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 338 SER 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 511 LEU 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 641 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 749 TYR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 809 MET 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 963 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 26 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 201 optimal weight: 20.0000 chunk 242 optimal weight: 7.9990 chunk 193 optimal weight: 0.8980 chunk 181 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 HIS ** 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 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 863 GLN ** 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 = 0.4905 r_free = 0.4905 target = 0.179452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.146049 restraints weight = 85217.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.144679 restraints weight = 52900.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.144338 restraints weight = 46385.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.145221 restraints weight = 38253.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.145902 restraints weight = 29950.309| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.7419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25230 Z= 0.116 Angle : 0.649 10.504 34078 Z= 0.335 Chirality : 0.044 0.191 3796 Planarity : 0.004 0.057 4332 Dihedral : 5.997 52.986 3371 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.10 % Favored : 92.44 % Rotamer: Outliers : 4.79 % Allowed : 28.34 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.15), residues: 3002 helix: -0.22 (0.15), residues: 1072 sheet: -0.73 (0.24), residues: 494 loop : -2.20 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 275 TYR 0.037 0.001 TYR A 741 PHE 0.021 0.001 PHE F 188 TRP 0.019 0.002 TRP D 8 HIS 0.026 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00249 (25230) covalent geometry : angle 0.64926 (34078) hydrogen bonds : bond 0.03555 ( 884) hydrogen bonds : angle 5.13398 ( 2520) *********************** 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 350 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 216 time to evaluate : 0.829 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: 0.1064 (tpp) cc_final: -0.1450 (ppp) REVERT: F 43 TRP cc_start: 0.4311 (t-100) cc_final: 0.4060 (t-100) REVERT: F 284 GLU cc_start: 0.4203 (OUTLIER) cc_final: 0.1207 (mt-10) REVERT: F 373 ASN cc_start: 0.8463 (m-40) cc_final: 0.7960 (m-40) REVERT: F 375 MET cc_start: 0.6788 (mmm) cc_final: 0.6442 (mmm) REVERT: E 177 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7924 (mp) REVERT: E 185 ARG cc_start: 0.6724 (mmp80) cc_final: 0.6303 (ptm-80) REVERT: E 199 ASN cc_start: 0.6590 (OUTLIER) cc_final: 0.5650 (m-40) REVERT: D 76 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6581 (tp) REVERT: D 492 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7775 (mtt) REVERT: D 605 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.7032 (tt) REVERT: D 611 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5765 (tt0) REVERT: D 808 THR cc_start: 0.6444 (p) cc_final: 0.6044 (p) REVERT: D 809 MET cc_start: 0.6769 (mmm) cc_final: 0.6475 (mmm) REVERT: D 828 THR cc_start: 0.6505 (OUTLIER) cc_final: 0.6135 (m) REVERT: D 853 MET cc_start: 0.5900 (OUTLIER) cc_final: 0.5057 (tpp) REVERT: D 858 ARG cc_start: -0.0059 (OUTLIER) cc_final: -0.3711 (ptp90) REVERT: D 891 MET cc_start: 0.3797 (tpp) cc_final: 0.3571 (tpp) REVERT: D 960 LEU cc_start: 0.1514 (OUTLIER) cc_final: 0.1194 (pp) REVERT: D 996 MET cc_start: 0.2908 (tpt) cc_final: 0.2617 (tpt) REVERT: C 25 SER cc_start: 0.7496 (t) cc_final: 0.6404 (p) REVERT: C 29 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5904 (tp30) REVERT: C 255 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.5732 (ptm-80) REVERT: C 257 LYS cc_start: 0.7145 (tptt) cc_final: 0.6421 (tmtt) REVERT: C 339 ASN cc_start: 0.6419 (t0) cc_final: 0.5727 (m-40) REVERT: C 376 ARG cc_start: 0.4268 (mmt180) cc_final: 0.2470 (tpt170) REVERT: C 414 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.5325 (m-80) REVERT: B 23 MET cc_start: 0.3908 (ppp) cc_final: 0.3035 (ptp) REVERT: B 158 LEU cc_start: 0.4942 (OUTLIER) cc_final: 0.4520 (mm) REVERT: A 158 ILE cc_start: -0.2463 (OUTLIER) cc_final: -0.2801 (pt) REVERT: A 230 MET cc_start: -0.2735 (ttp) cc_final: -0.3228 (ttm) REVERT: A 298 CYS cc_start: 0.4874 (m) cc_final: 0.4603 (p) REVERT: A 368 MET cc_start: 0.0291 (mtp) cc_final: -0.0374 (mmm) REVERT: A 640 MET cc_start: -0.0539 (OUTLIER) cc_final: -0.1041 (ppp) REVERT: A 707 LEU cc_start: 0.6894 (pt) cc_final: 0.6519 (tt) REVERT: A 842 MET cc_start: 0.0826 (mmp) cc_final: 0.0312 (tpt) REVERT: A 859 MET cc_start: 0.6845 (tpp) cc_final: 0.6473 (tmm) outliers start: 134 outliers final: 87 residues processed: 335 average time/residue: 0.1356 time to fit residues: 74.2630 Evaluate side-chains 303 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 199 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 129 PHE 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 284 GLU 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 356 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 37 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 155 LEU 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 178 VAL 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 48 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL 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 636 ARG Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 784 PHE 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 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 247 VAL Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 352 SER 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 17 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 THR 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 50 LEU 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 338 SER 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 470 TRP 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 608 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 MET 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 132 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 275 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS ** 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 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS A 225 GLN A 274 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.178444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.143453 restraints weight = 85944.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.141982 restraints weight = 45324.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.142758 restraints weight = 34464.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.142999 restraints weight = 28471.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.142996 restraints weight = 26493.856| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.7652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25230 Z= 0.141 Angle : 0.675 10.465 34078 Z= 0.351 Chirality : 0.045 0.212 3796 Planarity : 0.004 0.057 4332 Dihedral : 5.933 49.592 3366 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.83 % Favored : 91.71 % Rotamer: Outliers : 4.54 % Allowed : 28.59 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.15), residues: 3002 helix: -0.25 (0.15), residues: 1076 sheet: -0.71 (0.24), residues: 494 loop : -2.21 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 275 TYR 0.035 0.002 TYR A 741 PHE 0.029 0.002 PHE A 267 TRP 0.029 0.002 TRP D 470 HIS 0.006 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00314 (25230) covalent geometry : angle 0.67452 (34078) hydrogen bonds : bond 0.03764 ( 884) hydrogen bonds : angle 5.21589 ( 2520) *********************** 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 325 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 198 time to evaluate : 0.917 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: 0.1104 (tpp) cc_final: -0.1475 (ppp) REVERT: F 43 TRP cc_start: 0.4538 (t-100) cc_final: 0.4258 (t-100) REVERT: F 138 MET cc_start: 0.8181 (ttt) cc_final: 0.7949 (tpp) REVERT: F 284 GLU cc_start: 0.4668 (OUTLIER) cc_final: 0.1711 (mt-10) REVERT: F 373 ASN cc_start: 0.8421 (m-40) cc_final: 0.7965 (m-40) REVERT: F 375 MET cc_start: 0.6737 (mmm) cc_final: 0.6416 (mmm) REVERT: E 177 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7986 (mp) REVERT: E 185 ARG cc_start: 0.6538 (mmp80) cc_final: 0.6323 (ptt90) REVERT: D 60 MET cc_start: 0.7663 (mpp) cc_final: 0.7352 (mpp) REVERT: D 486 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7668 (m-10) REVERT: D 492 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7866 (mtt) REVERT: D 605 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7189 (tt) REVERT: D 611 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6169 (tt0) REVERT: D 808 THR cc_start: 0.6327 (p) cc_final: 0.5895 (p) REVERT: D 809 MET cc_start: 0.6607 (mmm) cc_final: 0.6389 (mmm) REVERT: D 828 THR cc_start: 0.6452 (OUTLIER) cc_final: 0.6106 (m) REVERT: D 853 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5298 (tpp) REVERT: D 891 MET cc_start: 0.4065 (tpp) cc_final: 0.3839 (tpp) REVERT: D 960 LEU cc_start: 0.1798 (OUTLIER) cc_final: 0.1473 (pp) REVERT: D 996 MET cc_start: 0.3075 (tpt) cc_final: 0.2853 (tpt) REVERT: C 1 MET cc_start: 0.4439 (tmm) cc_final: 0.3977 (mmm) REVERT: C 25 SER cc_start: 0.7690 (t) cc_final: 0.6507 (p) REVERT: C 29 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.5835 (tp30) REVERT: C 255 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5703 (ptm-80) REVERT: C 257 LYS cc_start: 0.7439 (tptt) cc_final: 0.6626 (tmtt) REVERT: C 339 ASN cc_start: 0.6442 (t0) cc_final: 0.5739 (m-40) REVERT: C 376 ARG cc_start: 0.4294 (mmt180) cc_final: 0.2543 (tpt170) REVERT: C 414 PHE cc_start: 0.5830 (OUTLIER) cc_final: 0.5446 (m-80) REVERT: B 23 MET cc_start: 0.3981 (ppp) cc_final: 0.3087 (ptp) REVERT: B 158 LEU cc_start: 0.5096 (OUTLIER) cc_final: 0.4679 (mm) REVERT: A 230 MET cc_start: -0.2652 (ttp) cc_final: -0.3167 (ttm) REVERT: A 368 MET cc_start: 0.0570 (mtp) cc_final: -0.0068 (mmm) REVERT: A 640 MET cc_start: -0.1190 (OUTLIER) cc_final: -0.1656 (ppp) REVERT: A 656 MET cc_start: -0.0209 (mmp) cc_final: -0.0815 (mmp) REVERT: A 800 MET cc_start: 0.3623 (ttt) cc_final: 0.3281 (ppp) REVERT: A 842 MET cc_start: 0.0853 (mmp) cc_final: 0.0336 (tpt) outliers start: 127 outliers final: 97 residues processed: 310 average time/residue: 0.1661 time to fit residues: 84.2779 Evaluate side-chains 303 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 192 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 129 PHE 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 208 GLN Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 284 GLU 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 356 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 155 LEU 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 178 VAL Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 48 GLN 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 106 GLU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 395 VAL 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 492 MET Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 572 VAL 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 636 ARG Chi-restraints excluded: chain D residue 641 LEU 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 837 LYS Chi-restraints excluded: chain D residue 853 MET 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 34 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 352 SER 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 17 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 THR 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 50 LEU 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 338 SER 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 511 LEU 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 692 ARG Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 MET 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 112 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 HIS ** 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** ** A 863 GLN ** 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 = 0.4887 r_free = 0.4887 target = 0.177690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.143926 restraints weight = 86796.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.142772 restraints weight = 50043.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.143593 restraints weight = 37563.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.143727 restraints weight = 31035.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.143819 restraints weight = 29325.377| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.7818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25230 Z= 0.141 Angle : 0.682 10.425 34078 Z= 0.353 Chirality : 0.045 0.199 3796 Planarity : 0.004 0.057 4332 Dihedral : 5.839 50.256 3362 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.66 % Favored : 91.87 % Rotamer: Outliers : 4.07 % Allowed : 28.95 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.15), residues: 3002 helix: -0.25 (0.15), residues: 1076 sheet: -0.69 (0.24), residues: 494 loop : -2.20 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 742 TYR 0.051 0.002 TYR A 741 PHE 0.038 0.002 PHE A 890 TRP 0.030 0.002 TRP D 470 HIS 0.009 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00315 (25230) covalent geometry : angle 0.68192 (34078) hydrogen bonds : bond 0.03697 ( 884) hydrogen bonds : angle 5.20293 ( 2520) ********************** 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: 114 poor density : 196 time to evaluate : 1.034 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: 0.1254 (tpp) cc_final: -0.1333 (ppp) REVERT: F 43 TRP cc_start: 0.4651 (t-100) cc_final: 0.4346 (t-100) REVERT: F 138 MET cc_start: 0.8206 (ttt) cc_final: 0.7986 (tpp) REVERT: F 189 ASP cc_start: 0.6778 (t0) cc_final: 0.6364 (m-30) REVERT: F 284 GLU cc_start: 0.4127 (OUTLIER) cc_final: 0.1333 (mt-10) REVERT: F 373 ASN cc_start: 0.8503 (m-40) cc_final: 0.8045 (m-40) REVERT: F 375 MET cc_start: 0.6835 (mmm) cc_final: 0.6430 (mmm) REVERT: E 177 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8047 (mp) REVERT: D 60 MET cc_start: 0.7905 (mpp) cc_final: 0.7481 (mpp) REVERT: D 492 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7879 (mtt) REVERT: D 611 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5973 (tt0) REVERT: D 714 PHE cc_start: 0.6632 (m-10) cc_final: 0.6408 (m-10) REVERT: D 808 THR cc_start: 0.6297 (p) cc_final: 0.5859 (p) REVERT: D 828 THR cc_start: 0.6318 (OUTLIER) cc_final: 0.5971 (m) REVERT: D 853 MET cc_start: 0.5951 (OUTLIER) cc_final: 0.5303 (tpp) REVERT: D 891 MET cc_start: 0.4064 (tpp) cc_final: 0.3834 (tpp) REVERT: D 960 LEU cc_start: 0.1768 (OUTLIER) cc_final: 0.1444 (pp) REVERT: D 996 MET cc_start: 0.3161 (tpt) cc_final: 0.2937 (tpt) REVERT: C 1 MET cc_start: 0.4710 (tmm) cc_final: 0.3845 (mmm) REVERT: C 25 SER cc_start: 0.7770 (t) cc_final: 0.6640 (p) REVERT: C 29 GLU cc_start: 0.5800 (OUTLIER) cc_final: 0.5587 (tp30) REVERT: C 255 ARG cc_start: 0.6206 (OUTLIER) cc_final: 0.5620 (ptm-80) REVERT: C 257 LYS cc_start: 0.7317 (tptt) cc_final: 0.6577 (tmtt) REVERT: C 339 ASN cc_start: 0.6415 (t0) cc_final: 0.5682 (m-40) REVERT: C 376 ARG cc_start: 0.4189 (mmt180) cc_final: 0.2396 (tpt170) REVERT: C 414 PHE cc_start: 0.5702 (OUTLIER) cc_final: 0.5321 (m-80) REVERT: B 23 MET cc_start: 0.3969 (ppp) cc_final: 0.3124 (ptp) REVERT: B 158 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4614 (mm) REVERT: A 230 MET cc_start: -0.2816 (ttp) cc_final: -0.3316 (ttm) REVERT: A 368 MET cc_start: 0.0851 (mtp) cc_final: 0.0197 (mmt) REVERT: A 640 MET cc_start: -0.1185 (OUTLIER) cc_final: -0.1681 (ppp) REVERT: A 656 MET cc_start: -0.0784 (mmp) cc_final: -0.1135 (mmp) REVERT: A 800 MET cc_start: 0.3278 (ttt) cc_final: 0.3066 (ppp) REVERT: A 842 MET cc_start: 0.0948 (mmp) cc_final: 0.0365 (tpt) REVERT: A 859 MET cc_start: 0.6484 (tmm) cc_final: 0.5981 (tmm) outliers start: 114 outliers final: 93 residues processed: 298 average time/residue: 0.1656 time to fit residues: 80.3084 Evaluate side-chains 294 residues out of total 2806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 189 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 284 GLU 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 370 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 155 LEU 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 199 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 48 GLN 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 106 GLU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 470 TRP Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 533 VAL 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 636 ARG Chi-restraints excluded: chain D residue 641 LEU 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 837 LYS Chi-restraints excluded: chain D residue 853 MET 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 34 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 352 SER 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 105 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 THR 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 50 LEU 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 338 SER 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 511 LEU 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 692 ARG Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 741 TYR Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 MET 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 158 optimal weight: 30.0000 chunk 231 optimal weight: 0.0070 chunk 54 optimal weight: 0.5980 chunk 216 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** 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 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** 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 = 0.4930 r_free = 0.4930 target = 0.189396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.156659 restraints weight = 86291.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.155074 restraints weight = 54855.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.155360 restraints weight = 39220.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.156039 restraints weight = 34502.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.156180 restraints weight = 29818.117| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.7936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25230 Z= 0.119 Angle : 0.671 13.969 34078 Z= 0.344 Chirality : 0.045 0.186 3796 Planarity : 0.004 0.056 4332 Dihedral : 5.585 51.848 3361 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.26 % Favored : 92.27 % Rotamer: Outliers : 3.36 % Allowed : 29.84 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.15), residues: 3002 helix: -0.06 (0.15), residues: 1072 sheet: -0.60 (0.24), residues: 492 loop : -2.10 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 742 TYR 0.044 0.001 TYR A 741 PHE 0.025 0.001 PHE F 215 TRP 0.020 0.002 TRP D 8 HIS 0.008 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00258 (25230) covalent geometry : angle 0.67114 (34078) hydrogen bonds : bond 0.03511 ( 884) hydrogen bonds : angle 5.09372 ( 2520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6520.75 seconds wall clock time: 113 minutes 2.43 seconds (6782.43 seconds total)