Starting phenix.real_space_refine on Sun Jan 26 14:13:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yrf_10888/01_2025/6yrf_10888.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yrf_10888/01_2025/6yrf_10888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6yrf_10888/01_2025/6yrf_10888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yrf_10888/01_2025/6yrf_10888.map" model { file = "/net/cci-nas-00/data/ceres_data/6yrf_10888/01_2025/6yrf_10888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yrf_10888/01_2025/6yrf_10888.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.171 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 68 5.16 5 C 15800 2.51 5 N 4036 2.21 5 O 4924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24828 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 6207 Classifications: {'peptide': 777} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 754} Chain: "B" Number of atoms: 6207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 6207 Classifications: {'peptide': 777} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 754} Restraints were copied for chains: C, D Time building chain proxies: 25.40, per 1000 atoms: 1.02 Number of scatterers: 24828 At special positions: 0 Unit cell: (169.335, 154.425, 168.27, 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 68 16.00 O 4924 8.00 N 4036 7.00 C 15800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.64 Conformation dependent library (CDL) restraints added in 3.0 seconds 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5840 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 42 sheets defined 34.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 30 through 48 Processing helix chain 'A' and resid 60 through 89 removed outlier: 3.523A pdb=" N GLY A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 161 removed outlier: 4.205A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 4.215A pdb=" N GLN A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 203 removed outlier: 3.953A pdb=" N LEU A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Proline residue: A 181 - end of helix removed outlier: 3.779A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.829A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.580A pdb=" N THR A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 Processing helix chain 'A' and resid 313 through 332 Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.844A pdb=" N GLU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 49 removed outlier: 3.673A pdb=" N GLY B 34 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 88 removed outlier: 3.531A pdb=" N ASP B 70 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 147 removed outlier: 5.661A pdb=" N LEU B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 129 - end of helix removed outlier: 3.664A pdb=" N LYS B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 162 removed outlier: 3.528A pdb=" N LYS B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 199 removed outlier: 3.588A pdb=" N ASN B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Proline residue: B 181 - end of helix removed outlier: 3.988A pdb=" N SER B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 231 removed outlier: 5.989A pdb=" N LEU B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 3.787A pdb=" N GLN B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 268 Processing helix chain 'B' and resid 276 through 306 Processing helix chain 'B' and resid 313 through 332 removed outlier: 3.744A pdb=" N ILE B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 406 through 412 removed outlier: 3.699A pdb=" N LEU B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 480 Processing helix chain 'B' and resid 531 through 538 removed outlier: 3.735A pdb=" N GLU B 538 " --> pdb=" O GLU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 610 removed outlier: 3.543A pdb=" N LEU B 610 " --> pdb=" O GLY B 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 610' Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 60 through 89 removed outlier: 3.523A pdb=" N GLY C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 161 removed outlier: 4.205A pdb=" N LEU C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Proline residue: C 129 - end of helix removed outlier: 4.215A pdb=" N GLN C 148 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 159 " --> pdb=" O GLN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 203 removed outlier: 3.953A pdb=" N LEU C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Proline residue: C 181 - end of helix removed outlier: 3.778A pdb=" N PHE C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.828A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 250 Processing helix chain 'C' and resid 257 through 267 removed outlier: 3.580A pdb=" N THR C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 305 Processing helix chain 'C' and resid 313 through 332 Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 531 through 538 removed outlier: 3.846A pdb=" N GLU C 538 " --> pdb=" O GLU C 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.673A pdb=" N GLY D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 49 " --> pdb=" O MET D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 88 removed outlier: 3.531A pdb=" N ASP D 70 " --> pdb=" O ASN D 66 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 147 removed outlier: 5.662A pdb=" N LEU D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Proline residue: D 129 - end of helix removed outlier: 3.665A pdb=" N LYS D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 162 removed outlier: 3.529A pdb=" N LYS D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 199 removed outlier: 3.587A pdb=" N ASN D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) Proline residue: D 181 - end of helix removed outlier: 3.988A pdb=" N SER D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 231 removed outlier: 5.990A pdb=" N LEU D 219 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 250 removed outlier: 3.787A pdb=" N GLN D 242 " --> pdb=" O GLU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 276 through 306 Processing helix chain 'D' and resid 313 through 332 removed outlier: 3.744A pdb=" N ILE D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 Processing helix chain 'D' and resid 406 through 412 removed outlier: 3.700A pdb=" N LEU D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 480 Processing helix chain 'D' and resid 531 through 538 removed outlier: 3.735A pdb=" N GLU D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 610 removed outlier: 3.542A pdb=" N LEU D 610 " --> pdb=" O GLY D 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 607 through 610' Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 340 removed outlier: 3.584A pdb=" N PHE A 340 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 528 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 344 through 348 removed outlier: 3.562A pdb=" N ILE A 495 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU A 368 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 386 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 370 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 469 removed outlier: 3.813A pdb=" N PHE A 453 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASN A 464 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N ALA A 451 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N VAL A 466 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 11.356A pdb=" N VAL A 449 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N VAL A 468 " --> pdb=" O TYR A 447 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N TYR A 447 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N LEU A 445 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS A 419 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N TYR A 447 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 462 through 469 removed outlier: 3.813A pdb=" N PHE A 453 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASN A 464 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N ALA A 451 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N VAL A 466 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 11.356A pdb=" N VAL A 449 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N VAL A 468 " --> pdb=" O TYR A 447 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N TYR A 447 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASN A 452 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE A 433 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 690 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 574 through 575 removed outlier: 3.586A pdb=" N PHE A 638 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 594 through 597 removed outlier: 5.363A pdb=" N GLY A 678 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LYS A 623 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN A 680 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL A 621 " --> pdb=" O ASN A 680 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLY A 624 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASP A 647 " --> pdb=" O GLY A 624 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.630A pdb=" N SER A 748 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 716 through 717 Processing sheet with id=AA9, first strand: chain 'A' and resid 735 through 738 Processing sheet with id=AB1, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AB2, first strand: chain 'B' and resid 344 through 348 removed outlier: 5.651A pdb=" N LEU B 368 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 386 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY B 370 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 381 " --> pdb=" O TYR B 404 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N GLU B 401 " --> pdb=" O GLU B 685 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N LYS B 687 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE B 403 " --> pdb=" O LYS B 687 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 344 through 348 removed outlier: 5.651A pdb=" N LEU B 368 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 386 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY B 370 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 381 " --> pdb=" O TYR B 404 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N GLU B 401 " --> pdb=" O GLU B 685 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N LYS B 687 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE B 403 " --> pdb=" O LYS B 687 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY B 678 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS B 623 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 680 " --> pdb=" O VAL B 621 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL B 621 " --> pdb=" O ASN B 680 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN B 615 " --> pdb=" O ILE B 686 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR B 616 " --> pdb=" O LYS B 653 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS B 653 " --> pdb=" O TYR B 616 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 618 " --> pdb=" O VAL B 651 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 651 " --> pdb=" O ILE B 618 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR B 620 " --> pdb=" O GLN B 649 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN B 649 " --> pdb=" O TYR B 620 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE B 622 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASP B 647 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 461 through 469 removed outlier: 3.784A pdb=" N PHE B 453 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASN B 464 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N ALA B 451 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 10.039A pdb=" N VAL B 466 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N VAL B 449 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N VAL B 468 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 11.386A pdb=" N TYR B 447 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS B 419 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N TYR B 447 " --> pdb=" O LYS B 419 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N TYR B 421 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N VAL B 449 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 461 through 469 removed outlier: 3.784A pdb=" N PHE B 453 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASN B 464 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N ALA B 451 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 10.039A pdb=" N VAL B 466 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N VAL B 449 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N VAL B 468 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 11.386A pdb=" N TYR B 447 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN B 452 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE B 433 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR B 454 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TYR B 431 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU B 690 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB7, first strand: chain 'B' and resid 574 through 575 removed outlier: 6.671A pdb=" N ILE B 628 " --> pdb=" O GLU B 639 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU B 639 " --> pdb=" O ILE B 628 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 630 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AB9, first strand: chain 'B' and resid 702 through 703 removed outlier: 3.644A pdb=" N PHE B 780 " --> pdb=" O ILE B 750 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 784 " --> pdb=" O ARG B 746 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 707 through 708 Processing sheet with id=AC2, first strand: chain 'B' and resid 769 through 770 removed outlier: 4.002A pdb=" N THR B 734 " --> pdb=" O GLU B 803 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 765 through 766 Processing sheet with id=AC4, first strand: chain 'C' and resid 339 through 340 removed outlier: 3.585A pdb=" N PHE C 340 " --> pdb=" O GLY C 528 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 528 " --> pdb=" O PHE C 340 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 344 through 348 removed outlier: 3.562A pdb=" N ILE C 495 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU C 368 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 386 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY C 370 " --> pdb=" O TYR C 384 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 462 through 469 removed outlier: 3.813A pdb=" N PHE C 453 " --> pdb=" O ASP C 462 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN C 464 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N ALA C 451 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N VAL C 466 " --> pdb=" O VAL C 449 " (cutoff:3.500A) removed outlier: 11.356A pdb=" N VAL C 449 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N VAL C 468 " --> pdb=" O TYR C 447 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N TYR C 447 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N LEU C 445 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS C 419 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N TYR C 447 " --> pdb=" O LYS C 419 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 462 through 469 removed outlier: 3.813A pdb=" N PHE C 453 " --> pdb=" O ASP C 462 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN C 464 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N ALA C 451 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N VAL C 466 " --> pdb=" O VAL C 449 " (cutoff:3.500A) removed outlier: 11.356A pdb=" N VAL C 449 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N VAL C 468 " --> pdb=" O TYR C 447 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N TYR C 447 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASN C 452 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE C 433 " --> pdb=" O ASN C 452 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 690 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 574 through 575 removed outlier: 3.586A pdb=" N PHE C 638 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 594 through 597 removed outlier: 5.363A pdb=" N GLY C 678 " --> pdb=" O LYS C 623 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS C 623 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASN C 680 " --> pdb=" O VAL C 621 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL C 621 " --> pdb=" O ASN C 680 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY C 624 " --> pdb=" O ASP C 647 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASP C 647 " --> pdb=" O GLY C 624 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 702 through 704 removed outlier: 3.630A pdb=" N SER C 748 " --> pdb=" O ALA C 782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 716 through 717 Processing sheet with id=AD3, first strand: chain 'C' and resid 735 through 738 Processing sheet with id=AD4, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AD5, first strand: chain 'D' and resid 344 through 348 removed outlier: 5.651A pdb=" N LEU D 368 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA D 386 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY D 370 " --> pdb=" O TYR D 384 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D 381 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N GLU D 401 " --> pdb=" O GLU D 685 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N LYS D 687 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE D 403 " --> pdb=" O LYS D 687 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 344 through 348 removed outlier: 5.651A pdb=" N LEU D 368 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA D 386 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY D 370 " --> pdb=" O TYR D 384 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D 381 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N GLU D 401 " --> pdb=" O GLU D 685 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N LYS D 687 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE D 403 " --> pdb=" O LYS D 687 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLY D 678 " --> pdb=" O LYS D 623 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS D 623 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN D 680 " --> pdb=" O VAL D 621 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL D 621 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN D 615 " --> pdb=" O ILE D 686 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR D 616 " --> pdb=" O LYS D 653 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS D 653 " --> pdb=" O TYR D 616 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE D 618 " --> pdb=" O VAL D 651 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 651 " --> pdb=" O ILE D 618 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR D 620 " --> pdb=" O GLN D 649 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN D 649 " --> pdb=" O TYR D 620 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE D 622 " --> pdb=" O ASP D 647 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASP D 647 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 461 through 469 removed outlier: 3.784A pdb=" N PHE D 453 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASN D 464 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N ALA D 451 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N VAL D 466 " --> pdb=" O VAL D 449 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N VAL D 449 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 10.183A pdb=" N VAL D 468 " --> pdb=" O TYR D 447 " (cutoff:3.500A) removed outlier: 11.386A pdb=" N TYR D 447 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS D 419 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N TYR D 447 " --> pdb=" O LYS D 419 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N TYR D 421 " --> pdb=" O TYR D 447 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N VAL D 449 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 461 through 469 removed outlier: 3.784A pdb=" N PHE D 453 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASN D 464 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N ALA D 451 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N VAL D 466 " --> pdb=" O VAL D 449 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N VAL D 449 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 10.183A pdb=" N VAL D 468 " --> pdb=" O TYR D 447 " (cutoff:3.500A) removed outlier: 11.386A pdb=" N TYR D 447 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN D 452 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE D 433 " --> pdb=" O ASN D 452 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR D 454 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TYR D 431 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU D 690 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AE1, first strand: chain 'D' and resid 574 through 575 removed outlier: 6.671A pdb=" N ILE D 628 " --> pdb=" O GLU D 639 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU D 639 " --> pdb=" O ILE D 628 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 630 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 702 through 703 Processing sheet with id=AE3, first strand: chain 'D' and resid 702 through 703 removed outlier: 3.643A pdb=" N PHE D 780 " --> pdb=" O ILE D 750 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D 784 " --> pdb=" O ARG D 746 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 707 through 708 Processing sheet with id=AE5, first strand: chain 'D' and resid 769 through 770 removed outlier: 4.002A pdb=" N THR D 734 " --> pdb=" O GLU D 803 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 765 through 766 1186 hydrogen bonds defined for protein. 3306 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: 10.31 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8087 1.34 - 1.46: 4865 1.46 - 1.57: 12200 1.57 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 25268 Sorted by residual: bond pdb=" CA LYS A 231 " pdb=" C LYS A 231 " ideal model delta sigma weight residual 1.524 1.473 0.051 2.25e-02 1.98e+03 5.08e+00 bond pdb=" CA LYS C 231 " pdb=" C LYS C 231 " ideal model delta sigma weight residual 1.524 1.474 0.050 2.25e-02 1.98e+03 4.93e+00 bond pdb=" N THR C 508 " pdb=" CA THR C 508 " ideal model delta sigma weight residual 1.457 1.430 0.027 1.41e-02 5.03e+03 3.58e+00 bond pdb=" N THR A 508 " pdb=" CA THR A 508 " ideal model delta sigma weight residual 1.457 1.430 0.026 1.41e-02 5.03e+03 3.53e+00 bond pdb=" CA GLU D 214 " pdb=" C GLU D 214 " ideal model delta sigma weight residual 1.524 1.505 0.018 1.27e-02 6.20e+03 2.11e+00 ... (remaining 25263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 33211 2.00 - 4.01: 810 4.01 - 6.01: 133 6.01 - 8.01: 20 8.01 - 10.01: 2 Bond angle restraints: 34176 Sorted by residual: angle pdb=" N MET C 234 " pdb=" CA MET C 234 " pdb=" C MET C 234 " ideal model delta sigma weight residual 110.91 116.30 -5.39 1.17e+00 7.31e-01 2.12e+01 angle pdb=" N MET A 234 " pdb=" CA MET A 234 " pdb=" C MET A 234 " ideal model delta sigma weight residual 110.91 116.27 -5.36 1.17e+00 7.31e-01 2.10e+01 angle pdb=" N ASP C 50 " pdb=" CA ASP C 50 " pdb=" C ASP C 50 " ideal model delta sigma weight residual 107.73 112.88 -5.15 1.34e+00 5.57e-01 1.48e+01 angle pdb=" N ASP A 50 " pdb=" CA ASP A 50 " pdb=" C ASP A 50 " ideal model delta sigma weight residual 107.73 112.87 -5.14 1.34e+00 5.57e-01 1.47e+01 angle pdb=" C ASN A 564 " pdb=" N ILE A 565 " pdb=" CA ILE A 565 " ideal model delta sigma weight residual 121.97 128.83 -6.86 1.80e+00 3.09e-01 1.45e+01 ... (remaining 34171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 13616 17.66 - 35.32: 1413 35.32 - 52.98: 216 52.98 - 70.64: 35 70.64 - 88.29: 20 Dihedral angle restraints: 15300 sinusoidal: 6216 harmonic: 9084 Sorted by residual: dihedral pdb=" CA VAL D 215 " pdb=" C VAL D 215 " pdb=" N ILE D 216 " pdb=" CA ILE D 216 " ideal model delta harmonic sigma weight residual 180.00 137.74 42.26 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CA VAL B 215 " pdb=" C VAL B 215 " pdb=" N ILE B 216 " pdb=" CA ILE B 216 " ideal model delta harmonic sigma weight residual 180.00 137.77 42.23 0 5.00e+00 4.00e-02 7.13e+01 dihedral pdb=" CA LYS B 213 " pdb=" C LYS B 213 " pdb=" N GLU B 214 " pdb=" CA GLU B 214 " ideal model delta harmonic sigma weight residual 180.00 148.07 31.93 0 5.00e+00 4.00e-02 4.08e+01 ... (remaining 15297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2948 0.050 - 0.100: 742 0.100 - 0.150: 182 0.150 - 0.201: 10 0.201 - 0.251: 2 Chirality restraints: 3884 Sorted by residual: chirality pdb=" CA PHE C 193 " pdb=" N PHE C 193 " pdb=" C PHE C 193 " pdb=" CB PHE C 193 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA PHE A 193 " pdb=" N PHE A 193 " pdb=" C PHE A 193 " pdb=" CB PHE A 193 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA THR D 180 " pdb=" N THR D 180 " pdb=" C THR D 180 " pdb=" CB THR D 180 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 3881 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 213 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C LYS B 213 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS B 213 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU B 214 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 213 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C LYS D 213 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS D 213 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU D 214 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 214 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C GLU B 214 " 0.030 2.00e-02 2.50e+03 pdb=" O GLU B 214 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL B 215 " -0.010 2.00e-02 2.50e+03 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 579 2.60 - 3.18: 25427 3.18 - 3.75: 42250 3.75 - 4.33: 57325 4.33 - 4.90: 88769 Nonbonded interactions: 214350 Sorted by model distance: nonbonded pdb=" O GLU B 201 " pdb=" OH TYR B 207 " model vdw 2.028 3.040 nonbonded pdb=" O GLU D 201 " pdb=" OH TYR D 207 " model vdw 2.028 3.040 nonbonded pdb=" O ASN B 203 " pdb=" OG SER B 206 " model vdw 2.108 3.040 nonbonded pdb=" O ASN D 203 " pdb=" OG SER D 206 " model vdw 2.108 3.040 nonbonded pdb=" OH TYR C 282 " pdb=" OD2 ASP C 540 " model vdw 2.141 3.040 ... (remaining 214345 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.860 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 66.540 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.006 0.057 25268 Z= 0.379 Angle : 0.783 10.014 34176 Z= 0.442 Chirality : 0.046 0.251 3884 Planarity : 0.004 0.042 4404 Dihedral : 14.496 88.294 9460 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 27.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.77 % Favored : 87.10 % Rotamer: Outliers : 0.21 % Allowed : 10.43 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.13), residues: 3100 helix: -0.63 (0.15), residues: 962 sheet: -2.60 (0.20), residues: 628 loop : -3.65 (0.13), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 471 HIS 0.008 0.002 HIS B 245 PHE 0.026 0.002 PHE C 193 TYR 0.021 0.002 TYR B 127 ARG 0.004 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8676 (tmm) cc_final: 0.8234 (tmm) REVERT: A 156 LEU cc_start: 0.8707 (tp) cc_final: 0.8454 (tp) REVERT: B 109 MET cc_start: 0.8306 (ttm) cc_final: 0.8096 (ttm) REVERT: B 134 MET cc_start: 0.8609 (tmm) cc_final: 0.8361 (tmm) REVERT: B 317 MET cc_start: 0.8782 (tmm) cc_final: 0.8494 (tmm) REVERT: C 134 MET cc_start: 0.8652 (tmm) cc_final: 0.8220 (tmm) REVERT: C 156 LEU cc_start: 0.8710 (tp) cc_final: 0.8457 (tp) REVERT: D 109 MET cc_start: 0.8389 (ttm) cc_final: 0.8157 (ttm) REVERT: D 134 MET cc_start: 0.8612 (tmm) cc_final: 0.8362 (tmm) REVERT: D 317 MET cc_start: 0.8766 (tmm) cc_final: 0.8468 (tmm) outliers start: 6 outliers final: 2 residues processed: 182 average time/residue: 0.3708 time to fit residues: 109.6979 Evaluate side-chains 99 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain D residue 156 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 4.9990 chunk 233 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 241 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 146 optimal weight: 30.0000 chunk 179 optimal weight: 0.7980 chunk 279 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 157 GLN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN A 577 ASN A 643 ASN A 725 GLN A 797 ASN B 30 ASN B 90 ASN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS C 157 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN C 577 ASN C 643 ASN C 725 GLN C 797 ASN D 30 ASN D 90 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** D 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 GLN ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.063208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.044282 restraints weight = 129555.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046089 restraints weight = 66375.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.047270 restraints weight = 43735.769| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25268 Z= 0.217 Angle : 0.686 9.528 34176 Z= 0.368 Chirality : 0.048 0.192 3884 Planarity : 0.004 0.047 4404 Dihedral : 6.285 67.389 3320 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 1.91 % Allowed : 14.22 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.15), residues: 3100 helix: 1.02 (0.17), residues: 982 sheet: -2.35 (0.19), residues: 646 loop : -3.03 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 471 HIS 0.007 0.002 HIS A 245 PHE 0.020 0.001 PHE A 254 TYR 0.015 0.001 TYR C 665 ARG 0.003 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 143 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8113 (t80) REVERT: A 58 LEU cc_start: 0.9064 (tp) cc_final: 0.8861 (tt) REVERT: A 134 MET cc_start: 0.8702 (tmm) cc_final: 0.8348 (tmm) REVERT: A 139 MET cc_start: 0.8097 (tpp) cc_final: 0.7885 (tpp) REVERT: B 43 MET cc_start: 0.8557 (mmt) cc_final: 0.8314 (mmt) REVERT: B 109 MET cc_start: 0.8409 (ttm) cc_final: 0.8185 (ttm) REVERT: B 124 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8067 (tt) REVERT: B 134 MET cc_start: 0.8428 (tmm) cc_final: 0.8082 (tmm) REVERT: B 220 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8421 (t0) REVERT: B 302 CYS cc_start: 0.8782 (m) cc_final: 0.8313 (m) REVERT: B 317 MET cc_start: 0.8716 (tmm) cc_final: 0.8375 (tmm) REVERT: B 674 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: B 695 MET cc_start: 0.8776 (mmm) cc_final: 0.8568 (mtp) REVERT: C 28 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8106 (t80) REVERT: C 134 MET cc_start: 0.8670 (tmm) cc_final: 0.8334 (tmm) REVERT: D 43 MET cc_start: 0.8553 (mmt) cc_final: 0.8311 (mmt) REVERT: D 109 MET cc_start: 0.8404 (ttm) cc_final: 0.8174 (ttm) REVERT: D 124 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8053 (tt) REVERT: D 134 MET cc_start: 0.8428 (tmm) cc_final: 0.8083 (tmm) REVERT: D 220 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8431 (t0) REVERT: D 302 CYS cc_start: 0.8775 (m) cc_final: 0.8302 (m) REVERT: D 317 MET cc_start: 0.8709 (tmm) cc_final: 0.8368 (tmm) REVERT: D 674 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8423 (m-80) REVERT: D 695 MET cc_start: 0.8765 (mmm) cc_final: 0.8561 (mtp) outliers start: 54 outliers final: 16 residues processed: 182 average time/residue: 0.3251 time to fit residues: 101.5182 Evaluate side-chains 132 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 112 HIS Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 674 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 280 optimal weight: 0.4980 chunk 70 optimal weight: 9.9990 chunk 203 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 264 optimal weight: 0.9990 chunk 301 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: