Starting phenix.real_space_refine on Mon Sep 30 09:09:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrf_10888/09_2024/6yrf_10888.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrf_10888/09_2024/6yrf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrf_10888/09_2024/6yrf_10888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrf_10888/09_2024/6yrf_10888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrf_10888/09_2024/6yrf_10888.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrf_10888/09_2024/6yrf_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 26.19, per 1000 atoms: 1.05 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: 6.74 Conformation dependent library (CDL) restraints added in 3.2 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: 4.22 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: 10.77 Time building geometry restraints manager: 7.75 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: 0.00 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: 1.040 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: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 70.190 Find NCS groups from input model: 0.830 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.360 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 6 poor density : 176 time to evaluate : 2.905 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: 0.3585 time to fit residues: 105.6035 Evaluate side-chains 99 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 3.042 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 fitting. rotamer outliers: 54 poor density : 143 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7934 (t80) REVERT: A 58 LEU cc_start: 0.9075 (tp) cc_final: 0.8861 (tt) REVERT: A 109 MET cc_start: 0.8639 (tpp) cc_final: 0.8438 (tmm) REVERT: A 134 MET cc_start: 0.8598 (tmm) cc_final: 0.8235 (tmm) REVERT: A 139 MET cc_start: 0.8146 (tpp) cc_final: 0.7926 (tpp) REVERT: B 109 MET cc_start: 0.8435 (ttm) cc_final: 0.8182 (ttm) REVERT: B 124 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8190 (tt) REVERT: B 134 MET cc_start: 0.8427 (tmm) cc_final: 0.8112 (tmm) REVERT: B 220 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8330 (t0) REVERT: B 302 CYS cc_start: 0.8702 (m) cc_final: 0.8336 (m) REVERT: B 317 MET cc_start: 0.8706 (tmm) cc_final: 0.8483 (tmm) REVERT: B 674 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: C 28 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7929 (t80) REVERT: C 58 LEU cc_start: 0.9069 (tp) cc_final: 0.8854 (tt) REVERT: C 109 MET cc_start: 0.8629 (tpp) cc_final: 0.8429 (tmm) REVERT: C 134 MET cc_start: 0.8591 (tmm) cc_final: 0.8240 (tmm) REVERT: C 139 MET cc_start: 0.8125 (tpp) cc_final: 0.7924 (tpp) REVERT: C 192 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8411 (mptt) REVERT: D 109 MET cc_start: 0.8426 (ttm) cc_final: 0.8163 (ttm) REVERT: D 124 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8180 (tt) REVERT: D 134 MET cc_start: 0.8426 (tmm) cc_final: 0.8112 (tmm) REVERT: D 220 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8314 (t0) REVERT: D 302 CYS cc_start: 0.8703 (m) cc_final: 0.8332 (m) REVERT: D 317 MET cc_start: 0.8707 (tmm) cc_final: 0.8482 (tmm) REVERT: D 674 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8420 (m-80) outliers start: 54 outliers final: 16 residues processed: 182 average time/residue: 0.3055 time to fit residues: 96.0639 Evaluate side-chains 133 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 2.994 ------------------------------------------------------------------------------- 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 155 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 232 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 280 optimal weight: 0.4980 chunk 302 optimal weight: 30.0000 chunk 249 optimal weight: 7.9990 chunk 277 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** 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 443 ASN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** 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 443 ASN ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25268 Z= 0.221 Angle : 0.654 8.628 34176 Z= 0.349 Chirality : 0.047 0.197 3884 Planarity : 0.004 0.044 4404 Dihedral : 6.041 64.038 3320 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 2.87 % Allowed : 15.53 % Favored : 81.60 % 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: -1.85 (0.15), residues: 3100 helix: 1.34 (0.17), residues: 992 sheet: -2.07 (0.20), residues: 626 loop : -2.74 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 471 HIS 0.007 0.001 HIS A 245 PHE 0.023 0.001 PHE A 254 TYR 0.014 0.001 TYR B 496 ARG 0.002 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 3 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 199 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 118 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7784 (t80) REVERT: A 58 LEU cc_start: 0.9058 (tp) cc_final: 0.8855 (tt) REVERT: A 139 MET cc_start: 0.8185 (tpp) cc_final: 0.7972 (tpp) REVERT: B 109 MET cc_start: 0.8449 (ttm) cc_final: 0.8196 (ttm) REVERT: B 124 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8207 (tt) REVERT: B 134 MET cc_start: 0.8430 (tmm) cc_final: 0.7987 (tmm) REVERT: B 139 MET cc_start: 0.8574 (tmm) cc_final: 0.8360 (tmm) REVERT: B 317 MET cc_start: 0.8771 (tmm) cc_final: 0.8525 (tmm) REVERT: B 674 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: C 28 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7788 (t80) REVERT: C 58 LEU cc_start: 0.9054 (tp) cc_final: 0.8834 (tt) REVERT: C 139 MET cc_start: 0.8166 (tpp) cc_final: 0.7932 (tpp) REVERT: D 109 MET cc_start: 0.8444 (ttm) cc_final: 0.8192 (ttm) REVERT: D 124 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8228 (tt) REVERT: D 134 MET cc_start: 0.8429 (tmm) cc_final: 0.8098 (tmm) REVERT: D 139 MET cc_start: 0.8574 (tmm) cc_final: 0.8358 (tmm) REVERT: D 317 MET cc_start: 0.8767 (tmm) cc_final: 0.8520 (tmm) REVERT: D 674 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8412 (m-80) outliers start: 81 outliers final: 39 residues processed: 187 average time/residue: 0.2958 time to fit residues: 96.3578 Evaluate side-chains 156 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 111 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 734 THR 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 175 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 734 THR 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 272 THR Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 801 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 20.0000 chunk 210 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 133 optimal weight: 40.0000 chunk 188 optimal weight: 4.9990 chunk 281 optimal weight: 6.9990 chunk 297 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 chunk 266 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** 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 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** 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 706 ASN ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25268 Z= 0.314 Angle : 0.699 8.842 34176 Z= 0.368 Chirality : 0.047 0.201 3884 Planarity : 0.004 0.044 4404 Dihedral : 6.157 63.311 3320 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 3.01 % Allowed : 18.83 % Favored : 78.16 % 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: -1.75 (0.15), residues: 3100 helix: 1.44 (0.17), residues: 964 sheet: -2.01 (0.19), residues: 654 loop : -2.63 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 471 HIS 0.009 0.002 HIS A 245 PHE 0.019 0.002 PHE D 254 TYR 0.017 0.001 TYR B 207 ARG 0.006 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 4 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 191 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 106 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7484 (t80) REVERT: A 515 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5435 (tt) REVERT: A 586 ASP cc_start: 0.9401 (p0) cc_final: 0.8960 (p0) REVERT: A 695 MET cc_start: 0.8953 (mpp) cc_final: 0.8419 (ptp) REVERT: B 109 MET cc_start: 0.8482 (ttm) cc_final: 0.8232 (ttm) REVERT: B 134 MET cc_start: 0.8497 (tmm) cc_final: 0.8063 (tmm) REVERT: B 139 MET cc_start: 0.8662 (tmm) cc_final: 0.8431 (tmm) REVERT: B 167 ASN cc_start: 0.8198 (t0) cc_final: 0.7980 (t0) REVERT: B 317 MET cc_start: 0.8840 (tmm) cc_final: 0.8621 (tmm) REVERT: B 674 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: C 28 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7487 (t80) REVERT: C 192 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8570 (mptt) REVERT: C 515 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5463 (tt) REVERT: C 586 ASP cc_start: 0.9395 (p0) cc_final: 0.8913 (p0) REVERT: C 695 MET cc_start: 0.8930 (mpp) cc_final: 0.8407 (ptp) REVERT: D 109 MET cc_start: 0.8473 (ttm) cc_final: 0.8230 (ttm) REVERT: D 134 MET cc_start: 0.8483 (tmm) cc_final: 0.8050 (tmm) REVERT: D 139 MET cc_start: 0.8663 (tmm) cc_final: 0.8431 (tmm) REVERT: D 167 ASN cc_start: 0.8148 (t0) cc_final: 0.7917 (t0) REVERT: D 317 MET cc_start: 0.8844 (tmm) cc_final: 0.8621 (tmm) REVERT: D 674 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.8533 (m-80) outliers start: 85 outliers final: 58 residues processed: 175 average time/residue: 0.3068 time to fit residues: 92.6811 Evaluate side-chains 168 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 104 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 734 THR 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 165 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain C residue 734 THR 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 165 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 207 TYR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 801 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 254 optimal weight: 0.9980 chunk 205 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25268 Z= 0.192 Angle : 0.641 15.058 34176 Z= 0.333 Chirality : 0.046 0.192 3884 Planarity : 0.003 0.048 4404 Dihedral : 5.751 58.012 3320 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 2.84 % Allowed : 19.93 % Favored : 77.23 % 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: -1.34 (0.15), residues: 3100 helix: 1.67 (0.17), residues: 986 sheet: -1.69 (0.20), residues: 630 loop : -2.40 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 471 HIS 0.006 0.001 HIS C 597 PHE 0.021 0.001 PHE A 193 TYR 0.009 0.001 TYR A 665 ARG 0.005 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 5 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 208 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 128 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.7491 (t80) REVERT: A 45 MET cc_start: 0.9060 (tmm) cc_final: 0.8708 (tmm) REVERT: A 381 LEU cc_start: 0.8967 (tp) cc_final: 0.8730 (tp) REVERT: A 515 LEU cc_start: 0.5979 (OUTLIER) cc_final: 0.5381 (tt) REVERT: A 587 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7834 (t) REVERT: B 109 MET cc_start: 0.8467 (ttm) cc_final: 0.8217 (ttm) REVERT: B 134 MET cc_start: 0.8415 (tmm) cc_final: 0.7996 (tmm) REVERT: B 139 MET cc_start: 0.8613 (tmm) cc_final: 0.8356 (tmm) REVERT: B 317 MET cc_start: 0.8775 (tmm) cc_final: 0.8556 (tmm) REVERT: B 674 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.8537 (m-80) REVERT: C 28 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7496 (t80) REVERT: C 43 MET cc_start: 0.7357 (mtm) cc_final: 0.7142 (ttm) REVERT: C 45 MET cc_start: 0.9048 (tmm) cc_final: 0.8693 (tmm) REVERT: C 192 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8407 (mptt) REVERT: C 381 LEU cc_start: 0.8960 (tp) cc_final: 0.8727 (tp) REVERT: C 515 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5400 (tt) REVERT: C 587 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7772 (t) REVERT: D 109 MET cc_start: 0.8463 (ttm) cc_final: 0.8208 (ttm) REVERT: D 134 MET cc_start: 0.8412 (tmm) cc_final: 0.7995 (tmm) REVERT: D 139 MET cc_start: 0.8614 (tmm) cc_final: 0.8353 (tmm) REVERT: D 317 MET cc_start: 0.8780 (tmm) cc_final: 0.8553 (tmm) REVERT: D 674 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8546 (m-80) outliers start: 80 outliers final: 43 residues processed: 191 average time/residue: 0.2939 time to fit residues: 97.7575 Evaluate side-chains 166 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 115 time to evaluate : 2.955 ------------------------------------------------------------------------------- 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 149 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 788 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 272 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 788 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 207 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 801 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.8980 chunk 268 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 73 optimal weight: 0.0000 chunk 298 optimal weight: 6.9990 chunk 247 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25268 Z= 0.184 Angle : 0.639 14.298 34176 Z= 0.334 Chirality : 0.045 0.196 3884 Planarity : 0.003 0.047 4404 Dihedral : 5.586 56.987 3320 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 3.19 % Allowed : 19.93 % Favored : 76.88 % 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: -1.18 (0.15), residues: 3100 helix: 1.73 (0.17), residues: 996 sheet: -1.51 (0.20), residues: 632 loop : -2.31 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 471 HIS 0.006 0.001 HIS A 597 PHE 0.021 0.001 PHE C 254 TYR 0.008 0.001 TYR A 665 ARG 0.006 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 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 223 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 133 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7465 (t80) REVERT: A 45 MET cc_start: 0.9065 (tmm) cc_final: 0.8693 (tmm) REVERT: A 97 LYS cc_start: 0.9582 (mttt) cc_final: 0.9348 (ptpp) REVERT: A 236 SER cc_start: 0.6779 (t) cc_final: 0.6296 (m) REVERT: A 381 LEU cc_start: 0.8922 (tp) cc_final: 0.8691 (tp) REVERT: A 515 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5364 (tt) REVERT: B 109 MET cc_start: 0.8428 (ttm) cc_final: 0.8199 (ttm) REVERT: B 124 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8236 (tt) REVERT: B 134 MET cc_start: 0.8381 (tmm) cc_final: 0.7984 (tmm) REVERT: B 139 MET cc_start: 0.8685 (tmm) cc_final: 0.8384 (tmm) REVERT: B 317 MET cc_start: 0.8775 (tmm) cc_final: 0.8562 (tmm) REVERT: B 578 ASN cc_start: 0.9088 (m-40) cc_final: 0.8671 (t0) REVERT: B 674 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8546 (m-80) REVERT: C 28 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7485 (t80) REVERT: C 45 MET cc_start: 0.9056 (tmm) cc_final: 0.8686 (tmm) REVERT: C 192 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8272 (mptt) REVERT: C 236 SER cc_start: 0.6789 (t) cc_final: 0.6296 (m) REVERT: C 248 MET cc_start: 0.9034 (tpt) cc_final: 0.8833 (tpt) REVERT: C 381 LEU cc_start: 0.8918 (tp) cc_final: 0.8689 (tp) REVERT: C 515 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5401 (tt) REVERT: C 695 MET cc_start: 0.8877 (mpp) cc_final: 0.8210 (ptp) REVERT: D 109 MET cc_start: 0.8426 (ttm) cc_final: 0.8172 (ttm) REVERT: D 124 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8229 (tt) REVERT: D 134 MET cc_start: 0.8381 (tmm) cc_final: 0.7983 (tmm) REVERT: D 139 MET cc_start: 0.8685 (tmm) cc_final: 0.8381 (tmm) REVERT: D 317 MET cc_start: 0.8772 (tmm) cc_final: 0.8557 (tmm) REVERT: D 578 ASN cc_start: 0.9096 (m-40) cc_final: 0.8682 (t0) REVERT: D 674 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8556 (m-80) outliers start: 90 outliers final: 51 residues processed: 213 average time/residue: 0.3093 time to fit residues: 112.4427 Evaluate side-chains 181 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 122 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 734 THR 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 175 THR Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 734 THR 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 175 THR Chi-restraints excluded: chain D residue 207 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 801 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 217 optimal weight: 0.0980 chunk 168 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 296 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 ASN A 270 ASN ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 320 HIS ** B 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 ASN C 270 ASN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS D 320 HIS ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25268 Z= 0.161 Angle : 0.633 15.661 34176 Z= 0.329 Chirality : 0.045 0.198 3884 Planarity : 0.003 0.050 4404 Dihedral : 5.378 55.493 3320 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.70 % Allowed : 20.50 % Favored : 76.81 % 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: -0.98 (0.15), residues: 3100 helix: 1.86 (0.17), residues: 998 sheet: -1.26 (0.20), residues: 650 loop : -2.25 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 471 HIS 0.006 0.001 HIS A 597 PHE 0.015 0.001 PHE C 254 TYR 0.008 0.001 TYR D 188 ARG 0.007 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 7 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 215 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 139 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7511 (t80) REVERT: A 43 MET cc_start: 0.7377 (ttm) cc_final: 0.6954 (ttm) REVERT: A 45 MET cc_start: 0.9047 (tmm) cc_final: 0.8702 (tmm) REVERT: A 97 LYS cc_start: 0.9571 (mttt) cc_final: 0.9349 (ptpp) REVERT: A 149 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8210 (mm) REVERT: A 236 SER cc_start: 0.6693 (t) cc_final: 0.6159 (m) REVERT: A 695 MET cc_start: 0.8396 (pmm) cc_final: 0.8093 (pmm) REVERT: B 109 MET cc_start: 0.8399 (ttm) cc_final: 0.8145 (ttm) REVERT: B 124 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8246 (tt) REVERT: B 134 MET cc_start: 0.8342 (tmm) cc_final: 0.7963 (tmm) REVERT: B 139 MET cc_start: 0.8614 (tmm) cc_final: 0.8316 (tmm) REVERT: B 317 MET cc_start: 0.8732 (tmm) cc_final: 0.8532 (tmm) REVERT: B 578 ASN cc_start: 0.9103 (m-40) cc_final: 0.8699 (t0) REVERT: B 674 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8527 (m-80) REVERT: C 28 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7519 (t80) REVERT: C 43 MET cc_start: 0.7426 (ttm) cc_final: 0.7177 (mtm) REVERT: C 45 MET cc_start: 0.9043 (tmm) cc_final: 0.8660 (tmm) REVERT: C 97 LYS cc_start: 0.9545 (mttt) cc_final: 0.9320 (ptpp) REVERT: C 149 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8209 (mm) REVERT: C 192 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8335 (mptt) REVERT: C 236 SER cc_start: 0.6699 (t) cc_final: 0.6161 (m) REVERT: C 381 LEU cc_start: 0.8843 (tp) cc_final: 0.8629 (tp) REVERT: C 695 MET cc_start: 0.8856 (mpp) cc_final: 0.8194 (ptp) REVERT: D 109 MET cc_start: 0.8398 (ttm) cc_final: 0.8155 (ttm) REVERT: D 124 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8239 (tt) REVERT: D 134 MET cc_start: 0.8336 (tmm) cc_final: 0.7959 (tmm) REVERT: D 139 MET cc_start: 0.8616 (tmm) cc_final: 0.8313 (tmm) REVERT: D 317 MET cc_start: 0.8731 (tmm) cc_final: 0.8527 (tmm) REVERT: D 578 ASN cc_start: 0.9113 (m-40) cc_final: 0.8705 (t0) REVERT: D 674 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8536 (m-80) outliers start: 76 outliers final: 53 residues processed: 206 average time/residue: 0.3076 time to fit residues: 108.2665 Evaluate side-chains 190 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 129 time to evaluate : 3.049 ------------------------------------------------------------------------------- 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 149 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain B residue 39 ILE 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 175 THR Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain D residue 39 ILE 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 175 THR Chi-restraints excluded: chain D residue 207 TYR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 801 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 188 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 HIS ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25268 Z= 0.213 Angle : 0.651 15.963 34176 Z= 0.337 Chirality : 0.046 0.211 3884 Planarity : 0.004 0.049 4404 Dihedral : 5.427 53.942 3320 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.70 % Allowed : 21.03 % Favored : 76.28 % 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: -0.93 (0.15), residues: 3100 helix: 1.86 (0.17), residues: 998 sheet: -1.24 (0.19), residues: 650 loop : -2.19 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 471 HIS 0.006 0.001 HIS A 245 PHE 0.014 0.001 PHE B 254 TYR 0.008 0.001 TYR C 511 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 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 202 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 126 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7360 (t80) REVERT: A 45 MET cc_start: 0.9056 (tmm) cc_final: 0.8665 (tmm) REVERT: A 97 LYS cc_start: 0.9577 (mttt) cc_final: 0.9358 (ptpp) REVERT: A 157 GLN cc_start: 0.8660 (mm-40) cc_final: 0.7988 (mm110) REVERT: A 236 SER cc_start: 0.6544 (t) cc_final: 0.6024 (m) REVERT: A 515 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5395 (tt) REVERT: A 695 MET cc_start: 0.8387 (pmm) cc_final: 0.8122 (pmm) REVERT: B 109 MET cc_start: 0.8429 (ttm) cc_final: 0.8198 (ttm) REVERT: B 124 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8222 (tt) REVERT: B 134 MET cc_start: 0.8454 (tmm) cc_final: 0.8034 (tmm) REVERT: B 139 MET cc_start: 0.8634 (tmm) cc_final: 0.8301 (tmm) REVERT: B 317 MET cc_start: 0.8778 (tmm) cc_final: 0.8570 (tmm) REVERT: B 578 ASN cc_start: 0.9117 (m-40) cc_final: 0.8731 (t0) REVERT: B 674 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: C 28 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7364 (t80) REVERT: C 45 MET cc_start: 0.9054 (tmm) cc_final: 0.8659 (tmm) REVERT: C 97 LYS cc_start: 0.9558 (mttt) cc_final: 0.9340 (ptpp) REVERT: C 157 GLN cc_start: 0.8654 (mm-40) cc_final: 0.7961 (mm110) REVERT: C 236 SER cc_start: 0.6551 (t) cc_final: 0.6033 (m) REVERT: C 381 LEU cc_start: 0.8849 (tp) cc_final: 0.8641 (tp) REVERT: C 515 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5344 (tt) REVERT: C 695 MET cc_start: 0.8864 (mpp) cc_final: 0.8425 (ptp) REVERT: D 109 MET cc_start: 0.8428 (ttm) cc_final: 0.8215 (ttm) REVERT: D 124 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8220 (tt) REVERT: D 134 MET cc_start: 0.8448 (tmm) cc_final: 0.8031 (tmm) REVERT: D 139 MET cc_start: 0.8646 (tmm) cc_final: 0.8313 (tmm) REVERT: D 317 MET cc_start: 0.8777 (tmm) cc_final: 0.8564 (tmm) REVERT: D 578 ASN cc_start: 0.9130 (m-40) cc_final: 0.8744 (t0) REVERT: D 674 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8590 (m-80) outliers start: 76 outliers final: 55 residues processed: 192 average time/residue: 0.3131 time to fit residues: 102.3451 Evaluate side-chains 182 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 119 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain B residue 39 ILE 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 175 THR Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain D residue 39 ILE 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 175 THR Chi-restraints excluded: chain D residue 207 TYR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 801 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 20.0000 chunk 284 optimal weight: 0.0670 chunk 259 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 166 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 217 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 249 optimal weight: 0.0970 chunk 261 optimal weight: 7.9990 chunk 275 optimal weight: 10.0000 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** B 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN C 292 GLN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25268 Z= 0.155 Angle : 0.638 16.015 34176 Z= 0.329 Chirality : 0.046 0.194 3884 Planarity : 0.004 0.059 4404 Dihedral : 5.180 51.766 3320 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.52 % Allowed : 21.56 % Favored : 75.92 % 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: -0.77 (0.15), residues: 3100 helix: 1.94 (0.17), residues: 988 sheet: -1.10 (0.19), residues: 656 loop : -2.04 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 471 HIS 0.006 0.001 HIS A 597 PHE 0.017 0.001 PHE D 239 TYR 0.009 0.001 TYR B 188 ARG 0.004 0.000 ARG B 714 *********************** REFINEMENT MACRO_CYCLE 9 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 215 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 144 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7297 (ttm) cc_final: 0.6904 (ttm) REVERT: A 45 MET cc_start: 0.9025 (tmm) cc_final: 0.8605 (tmm) REVERT: A 57 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7090 (p) REVERT: A 97 LYS cc_start: 0.9599 (mttt) cc_final: 0.9380 (ptpp) REVERT: A 165 ILE cc_start: 0.7862 (mm) cc_final: 0.7654 (tp) REVERT: A 236 SER cc_start: 0.6301 (t) cc_final: 0.5801 (m) REVERT: A 381 LEU cc_start: 0.8630 (tp) cc_final: 0.8428 (tp) REVERT: A 587 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7524 (t) REVERT: A 695 MET cc_start: 0.8249 (pmm) cc_final: 0.7985 (pmm) REVERT: B 109 MET cc_start: 0.8392 (ttm) cc_final: 0.8170 (ttm) REVERT: B 124 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8278 (tt) REVERT: B 134 MET cc_start: 0.8348 (tmm) cc_final: 0.7951 (tmm) REVERT: B 139 MET cc_start: 0.8522 (tmm) cc_final: 0.8203 (tmm) REVERT: B 381 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7829 (tp) REVERT: B 578 ASN cc_start: 0.9114 (m-40) cc_final: 0.8812 (t0) REVERT: B 674 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8515 (m-80) REVERT: C 43 MET cc_start: 0.7304 (ttm) cc_final: 0.7029 (ttp) REVERT: C 45 MET cc_start: 0.9022 (tmm) cc_final: 0.8677 (tmm) REVERT: C 57 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7136 (p) REVERT: C 97 LYS cc_start: 0.9592 (mttt) cc_final: 0.9374 (ptpp) REVERT: C 165 ILE cc_start: 0.7866 (mm) cc_final: 0.7649 (tp) REVERT: C 236 SER cc_start: 0.6299 (t) cc_final: 0.5803 (m) REVERT: C 587 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7542 (t) REVERT: C 695 MET cc_start: 0.8823 (mpp) cc_final: 0.8129 (ptp) REVERT: D 109 MET cc_start: 0.8399 (ttm) cc_final: 0.8153 (ttm) REVERT: D 124 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8276 (tt) REVERT: D 134 MET cc_start: 0.8348 (tmm) cc_final: 0.7955 (tmm) REVERT: D 139 MET cc_start: 0.8524 (tmm) cc_final: 0.8206 (tmm) REVERT: D 381 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7818 (tp) REVERT: D 578 ASN cc_start: 0.9121 (m-40) cc_final: 0.8816 (t0) REVERT: D 674 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.8524 (m-80) outliers start: 71 outliers final: 45 residues processed: 202 average time/residue: 0.3115 time to fit residues: 107.2615 Evaluate side-chains 187 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 132 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 734 THR 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 175 THR Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 587 THR 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 175 THR Chi-restraints excluded: chain D residue 207 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 801 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 2.9990 chunk 292 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 306 optimal weight: 5.9990 chunk 282 optimal weight: 0.0370 chunk 244 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3912 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= 0.171 Angle : 0.651 16.674 34176 Z= 0.333 Chirality : 0.046 0.253 3884 Planarity : 0.004 0.043 4404 Dihedral : 5.156 51.091 3320 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 2.02 % Allowed : 22.27 % Favored : 75.71 % 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: -0.71 (0.15), residues: 3100 helix: 1.97 (0.17), residues: 994 sheet: -1.00 (0.19), residues: 674 loop : -2.05 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 471 HIS 0.006 0.001 HIS A 597 PHE 0.020 0.001 PHE D 239 TYR 0.008 0.001 TYR A 547 ARG 0.003 0.000 ARG C 256 ********************** REFINEMENT MACRO_CYCLE 10 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 185 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 128 time to evaluate : 2.977 Fit side-chains revert: symmetry clash REVERT: A 45 MET cc_start: 0.8999 (tmm) cc_final: 0.8612 (tmm) REVERT: A 97 LYS cc_start: 0.9596 (mttt) cc_final: 0.9373 (ptpp) REVERT: A 157 GLN cc_start: 0.8554 (mm-40) cc_final: 0.7853 (mm110) REVERT: A 236 SER cc_start: 0.6766 (t) cc_final: 0.6151 (m) REVERT: A 695 MET cc_start: 0.8347 (pmm) cc_final: 0.8090 (pmm) REVERT: B 109 MET cc_start: 0.8384 (ttm) cc_final: 0.8137 (ttm) REVERT: B 124 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8295 (tt) REVERT: B 134 MET cc_start: 0.8419 (tmm) cc_final: 0.8079 (tmm) REVERT: B 139 MET cc_start: 0.8474 (tmm) cc_final: 0.8160 (tmm) REVERT: B 381 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7851 (tp) REVERT: B 578 ASN cc_start: 0.9112 (m-40) cc_final: 0.8824 (t0) REVERT: B 674 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8527 (m-80) REVERT: B 695 MET cc_start: 0.8190 (pmm) cc_final: 0.7944 (pmm) REVERT: C 43 MET cc_start: 0.7291 (ttm) cc_final: 0.6955 (ttp) REVERT: C 45 MET cc_start: 0.9021 (tmm) cc_final: 0.8643 (tmm) REVERT: C 97 LYS cc_start: 0.9589 (mttt) cc_final: 0.9370 (ptpp) REVERT: C 157 GLN cc_start: 0.8527 (mm-40) cc_final: 0.7821 (mm110) REVERT: C 236 SER cc_start: 0.6929 (t) cc_final: 0.6396 (m) REVERT: D 109 MET cc_start: 0.8371 (ttm) cc_final: 0.8141 (ttm) REVERT: D 124 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8293 (tt) REVERT: D 134 MET cc_start: 0.8406 (tmm) cc_final: 0.7980 (tmm) REVERT: D 139 MET cc_start: 0.8479 (tmm) cc_final: 0.8163 (tmm) REVERT: D 381 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7824 (tp) REVERT: D 578 ASN cc_start: 0.9120 (m-40) cc_final: 0.8826 (t0) REVERT: D 674 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: D 695 MET cc_start: 0.8188 (pmm) cc_final: 0.7939 (pmm) outliers start: 57 outliers final: 41 residues processed: 174 average time/residue: 0.3098 time to fit residues: 92.7305 Evaluate side-chains 169 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 122 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 734 THR 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 175 THR Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 734 THR 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 175 THR Chi-restraints excluded: chain D residue 207 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 801 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 225 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 0.0570 chunk 102 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.0470 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.065677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.046816 restraints weight = 132092.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.048729 restraints weight = 66264.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.049966 restraints weight = 43150.887| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25268 Z= 0.162 Angle : 0.655 16.667 34176 Z= 0.332 Chirality : 0.045 0.194 3884 Planarity : 0.003 0.039 4404 Dihedral : 5.107 49.780 3320 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 2.27 % Allowed : 22.27 % Favored : 75.46 % 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: -0.67 (0.15), residues: 3100 helix: 1.99 (0.16), residues: 998 sheet: -0.89 (0.19), residues: 674 loop : -2.07 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 471 HIS 0.006 0.001 HIS A 597 PHE 0.019 0.001 PHE D 239 TYR 0.014 0.001 TYR D 282 ARG 0.003 0.000 ARG A 714 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3857.95 seconds wall clock time: 71 minutes 52.60 seconds (4312.60 seconds total)