Starting phenix.real_space_refine on Thu Mar 5 19:43:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yrf_10888/03_2026/6yrf_10888.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yrf_10888/03_2026/6yrf_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 { model { file = "/net/cci-nas-00/data/ceres_data/6yrf_10888/03_2026/6yrf_10888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yrf_10888/03_2026/6yrf_10888.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yrf_10888/03_2026/6yrf_10888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yrf_10888/03_2026/6yrf_10888.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 10.73, per 1000 atoms: 0.43 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: 1.90 Conformation dependent library (CDL) restraints added in 1.0 seconds 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5840 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 42 sheets defined 34.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 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: 5.47 Time building geometry restraints manager: 2.62 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: 0.02 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: 1.130 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.660 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.240 ------------------------------------------------------------------------------- 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= 0.285 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 : 27.46 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG C 185 TYR 0.021 0.002 TYR B 127 PHE 0.026 0.002 PHE C 193 TRP 0.014 0.002 TRP B 471 HIS 0.008 0.002 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00585 (25268) covalent geometry : angle 0.78280 (34176) hydrogen bonds : bond 0.21647 ( 1134) hydrogen bonds : angle 8.56886 ( 3306) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8675 (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: 0.8156 (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: 0.1555 time to fit residues: 46.3597 Evaluate side-chains 100 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 155 GLN ** 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 B 671 GLN B 725 GLN 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 319 HIS ** 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN 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 D 671 GLN D 725 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.063320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.044276 restraints weight = 130635.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.046109 restraints weight = 66508.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047300 restraints weight = 43706.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.048056 restraints weight = 33457.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.048561 restraints weight = 28244.710| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1821 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= 0.160 Angle : 0.682 9.773 34176 Z= 0.365 Chirality : 0.048 0.192 3884 Planarity : 0.004 0.049 4404 Dihedral : 6.255 66.994 3320 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 1.81 % Allowed : 14.22 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.15), residues: 3100 helix: 1.03 (0.17), residues: 982 sheet: -2.32 (0.19), residues: 646 loop : -3.02 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 326 TYR 0.015 0.001 TYR C 665 PHE 0.019 0.001 PHE A 254 TRP 0.013 0.001 TRP B 471 HIS 0.007 0.002 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00340 (25268) covalent geometry : angle 0.68175 (34176) hydrogen bonds : bond 0.04830 ( 1134) hydrogen bonds : angle 6.26107 ( 3306) *********************** 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 199 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8122 (t80) REVERT: A 58 LEU cc_start: 0.9083 (tp) cc_final: 0.8878 (tt) REVERT: A 134 MET cc_start: 0.8647 (tmm) cc_final: 0.8343 (tmm) REVERT: A 139 MET cc_start: 0.8046 (tpp) cc_final: 0.7843 (tpp) REVERT: B 43 MET cc_start: 0.8544 (mmt) cc_final: 0.8321 (mmt) REVERT: B 109 MET cc_start: 0.8379 (ttm) cc_final: 0.8168 (ttm) REVERT: B 124 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8026 (tt) REVERT: B 134 MET cc_start: 0.8393 (tmm) cc_final: 0.8038 (tmm) REVERT: B 220 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8454 (t0) REVERT: B 302 CYS cc_start: 0.8841 (m) cc_final: 0.8315 (m) REVERT: B 317 MET cc_start: 0.8747 (tmm) cc_final: 0.8385 (tmm) REVERT: B 674 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.8423 (m-80) REVERT: B 695 MET cc_start: 0.8836 (mmm) cc_final: 0.8585 (mtp) REVERT: C 28 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8117 (t80) REVERT: C 58 LEU cc_start: 0.9083 (tp) cc_final: 0.8869 (tt) REVERT: C 134 MET cc_start: 0.8622 (tmm) cc_final: 0.8302 (tmm) REVERT: D 43 MET cc_start: 0.8540 (mmt) cc_final: 0.8320 (mmt) REVERT: D 109 MET cc_start: 0.8385 (ttm) cc_final: 0.8156 (ttm) REVERT: D 124 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7998 (tt) REVERT: D 134 MET cc_start: 0.8395 (tmm) cc_final: 0.8038 (tmm) REVERT: D 220 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8480 (t0) REVERT: D 302 CYS cc_start: 0.8851 (m) cc_final: 0.8323 (m) REVERT: D 317 MET cc_start: 0.8744 (tmm) cc_final: 0.8379 (tmm) REVERT: D 674 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: D 695 MET cc_start: 0.8832 (mmm) cc_final: 0.8584 (mtp) outliers start: 51 outliers final: 16 residues processed: 185 average time/residue: 0.1401 time to fit residues: 44.5278 Evaluate side-chains 137 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 7 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 292 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 303 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 173 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 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN A 643 ASN ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** 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** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 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 106 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.061701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.042677 restraints weight = 134256.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.044377 restraints weight = 70127.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.045470 restraints weight = 46930.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.046177 restraints weight = 36439.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.046637 restraints weight = 30981.255| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25268 Z= 0.224 Angle : 0.707 8.382 34176 Z= 0.375 Chirality : 0.048 0.201 3884 Planarity : 0.004 0.041 4404 Dihedral : 6.247 66.359 3320 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 3.05 % Allowed : 16.74 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.15), residues: 3100 helix: 1.25 (0.17), residues: 980 sheet: -2.19 (0.19), residues: 634 loop : -2.78 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 533 TYR 0.013 0.001 TYR D 674 PHE 0.021 0.002 PHE C 193 TRP 0.010 0.001 TRP B 471 HIS 0.009 0.002 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00489 (25268) covalent geometry : angle 0.70739 (34176) hydrogen bonds : bond 0.04929 ( 1134) hydrogen bonds : angle 6.03243 ( 3306) *********************** 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 198 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 112 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7648 (t80) REVERT: A 134 MET cc_start: 0.8676 (tmm) cc_final: 0.8370 (tmm) REVERT: A 139 MET cc_start: 0.8178 (tpp) cc_final: 0.7903 (tpp) REVERT: B 43 MET cc_start: 0.8618 (mmt) cc_final: 0.8284 (mmt) REVERT: B 109 MET cc_start: 0.8420 (ttm) cc_final: 0.8218 (ttm) REVERT: B 134 MET cc_start: 0.8460 (tmm) cc_final: 0.8208 (tmm) REVERT: B 139 MET cc_start: 0.8571 (tmm) cc_final: 0.8352 (tmm) REVERT: B 317 MET cc_start: 0.8889 (tmm) cc_final: 0.8496 (tmm) REVERT: B 380 ILE cc_start: 0.8740 (mt) cc_final: 0.8499 (mm) REVERT: B 674 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8484 (m-80) REVERT: B 695 MET cc_start: 0.8938 (mmm) cc_final: 0.8696 (mtp) REVERT: C 28 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.7643 (t80) REVERT: D 43 MET cc_start: 0.8616 (mmt) cc_final: 0.8280 (mmt) REVERT: D 134 MET cc_start: 0.8464 (tmm) cc_final: 0.7995 (tmm) REVERT: D 139 MET cc_start: 0.8601 (tmm) cc_final: 0.8353 (tmm) REVERT: D 317 MET cc_start: 0.8881 (tmm) cc_final: 0.8493 (tmm) REVERT: D 380 ILE cc_start: 0.8748 (mt) cc_final: 0.8503 (mm) REVERT: D 674 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: D 695 MET cc_start: 0.8933 (mmm) cc_final: 0.8695 (mtp) outliers start: 86 outliers final: 44 residues processed: 183 average time/residue: 0.1379 time to fit residues: 44.8198 Evaluate side-chains 150 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 403 ILE Chi-restraints excluded: chain A residue 584 LYS 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 249 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 584 LYS 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 249 THR 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 30 optimal weight: 2.9990 chunk 284 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 225 optimal weight: 30.0000 chunk 128 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 300 optimal weight: 40.0000 chunk 145 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 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 106 GLN ** 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 319 HIS B 320 HIS ** B 342 ASN ** 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 ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS D 319 HIS D 320 HIS ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.064168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.045286 restraints weight = 129679.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.047097 restraints weight = 65997.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.048262 restraints weight = 43498.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.049030 restraints weight = 33344.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.049489 restraints weight = 28106.074| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2705 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= 0.126 Angle : 0.632 13.756 34176 Z= 0.332 Chirality : 0.046 0.191 3884 Planarity : 0.004 0.048 4404 Dihedral : 5.777 59.357 3320 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 2.70 % Allowed : 18.23 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.15), residues: 3100 helix: 1.66 (0.17), residues: 992 sheet: -1.82 (0.20), residues: 638 loop : -2.55 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.010 0.001 TYR C 665 PHE 0.018 0.001 PHE A 254 TRP 0.011 0.001 TRP B 471 HIS 0.006 0.001 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00261 (25268) covalent geometry : angle 0.63176 (34176) hydrogen bonds : bond 0.04188 ( 1134) hydrogen bonds : angle 5.56390 ( 3306) *********************** 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 207 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 131 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.7667 (t80) REVERT: A 45 MET cc_start: 0.8966 (tmm) cc_final: 0.8629 (tmm) REVERT: A 515 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5282 (tt) REVERT: A 709 MET cc_start: 0.8887 (pmm) cc_final: 0.8679 (ttm) REVERT: B 43 MET cc_start: 0.8499 (mmt) cc_final: 0.8251 (mmt) REVERT: B 109 MET cc_start: 0.8403 (ttm) cc_final: 0.8190 (ttm) REVERT: B 124 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8157 (tt) REVERT: B 134 MET cc_start: 0.8360 (tmm) cc_final: 0.8039 (tmm) REVERT: B 139 MET cc_start: 0.8629 (tmm) cc_final: 0.8358 (tmm) REVERT: B 231 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8600 (tmtt) REVERT: B 317 MET cc_start: 0.8814 (tmm) cc_final: 0.8447 (tmm) REVERT: B 674 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8485 (m-80) REVERT: C 28 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7654 (t80) REVERT: C 45 MET cc_start: 0.8968 (tmm) cc_final: 0.8638 (tmm) REVERT: C 134 MET cc_start: 0.8625 (tmm) cc_final: 0.8407 (tmm) REVERT: C 515 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5324 (tt) REVERT: D 43 MET cc_start: 0.8495 (mmt) cc_final: 0.8232 (mmt) REVERT: D 124 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8162 (tt) REVERT: D 134 MET cc_start: 0.8351 (tmm) cc_final: 0.8033 (tmm) REVERT: D 139 MET cc_start: 0.8604 (tmm) cc_final: 0.8326 (tmm) REVERT: D 231 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8581 (tmtt) REVERT: D 317 MET cc_start: 0.8810 (tmm) cc_final: 0.8437 (tmm) REVERT: D 674 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8489 (m-80) outliers start: 76 outliers final: 36 residues processed: 193 average time/residue: 0.1350 time to fit residues: 45.8751 Evaluate side-chains 163 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 199 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 359 VAL 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 165 ILE 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 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 278 ILE Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 359 VAL 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 165 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 359 VAL 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 137 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 235 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 279 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 300 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 278 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 210 ASN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 GLN B 706 ASN ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 444 GLN D 706 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.060000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.041030 restraints weight = 140687.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.042634 restraints weight = 75801.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.043669 restraints weight = 51489.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.044318 restraints weight = 40279.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.044760 restraints weight = 34490.601| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 25268 Z= 0.322 Angle : 0.794 14.382 34176 Z= 0.414 Chirality : 0.049 0.225 3884 Planarity : 0.004 0.039 4404 Dihedral : 6.321 61.349 3320 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.19 % Favored : 88.74 % Rotamer: Outliers : 3.37 % Allowed : 20.53 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.15), residues: 3100 helix: 1.22 (0.16), residues: 998 sheet: -1.85 (0.19), residues: 676 loop : -2.55 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 746 TYR 0.015 0.002 TYR C 511 PHE 0.027 0.002 PHE C 193 TRP 0.012 0.002 TRP C 701 HIS 0.011 0.002 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00701 (25268) covalent geometry : angle 0.79412 (34176) hydrogen bonds : bond 0.05259 ( 1134) hydrogen bonds : angle 5.92309 ( 3306) *********************** 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 206 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 111 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.9570 (mttt) cc_final: 0.9370 (ptpp) REVERT: A 157 GLN cc_start: 0.8587 (mm-40) cc_final: 0.7900 (mm110) REVERT: A 210 ASN cc_start: 0.6963 (OUTLIER) cc_final: 0.6459 (t0) REVERT: A 586 ASP cc_start: 0.9429 (p0) cc_final: 0.9002 (p0) REVERT: B 43 MET cc_start: 0.8733 (mmt) cc_final: 0.8376 (mmt) REVERT: B 109 MET cc_start: 0.8447 (ttm) cc_final: 0.8247 (ttm) REVERT: B 134 MET cc_start: 0.8543 (tmm) cc_final: 0.8315 (tmm) REVERT: B 139 MET cc_start: 0.8650 (tmm) cc_final: 0.8373 (tmm) REVERT: B 317 MET cc_start: 0.8991 (tmm) cc_final: 0.8600 (tmm) REVERT: B 674 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8617 (m-80) REVERT: C 97 LYS cc_start: 0.9572 (mttt) cc_final: 0.9369 (ptpp) REVERT: C 134 MET cc_start: 0.8654 (tmm) cc_final: 0.8435 (tmm) REVERT: C 157 GLN cc_start: 0.8607 (mm-40) cc_final: 0.7937 (mm110) REVERT: C 210 ASN cc_start: 0.6949 (OUTLIER) cc_final: 0.6460 (t0) REVERT: C 586 ASP cc_start: 0.9439 (p0) cc_final: 0.9018 (p0) REVERT: D 43 MET cc_start: 0.8731 (mmt) cc_final: 0.8373 (mmt) REVERT: D 134 MET cc_start: 0.8539 (tmm) cc_final: 0.8315 (tmm) REVERT: D 139 MET cc_start: 0.8662 (tmm) cc_final: 0.8392 (tmm) REVERT: D 317 MET cc_start: 0.8989 (tmm) cc_final: 0.8578 (tmm) REVERT: D 674 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8620 (m-80) outliers start: 95 outliers final: 62 residues processed: 191 average time/residue: 0.1436 time to fit residues: 47.5120 Evaluate side-chains 168 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 102 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 194 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 606 ILE 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 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 359 VAL 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 32 ILE 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 195 GLU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 298 THR 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 381 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 606 ILE 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 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 359 VAL 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 59 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 262 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 300 optimal weight: 40.0000 chunk 92 optimal weight: 2.9990 chunk 292 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 210 ASN ** 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 342 ASN ** 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 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 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 444 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.062595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.043626 restraints weight = 135442.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.045352 restraints weight = 71331.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.046444 restraints weight = 47754.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.047193 restraints weight = 37047.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.047661 restraints weight = 31359.690| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2928 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= 0.143 Angle : 0.662 11.804 34176 Z= 0.345 Chirality : 0.046 0.194 3884 Planarity : 0.004 0.046 4404 Dihedral : 5.884 57.125 3320 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 3.26 % Allowed : 20.71 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.15), residues: 3100 helix: 1.66 (0.17), residues: 982 sheet: -1.70 (0.20), residues: 630 loop : -2.40 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 746 TYR 0.010 0.001 TYR D 674 PHE 0.014 0.001 PHE C 193 TRP 0.012 0.001 TRP B 471 HIS 0.006 0.001 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00306 (25268) covalent geometry : angle 0.66159 (34176) hydrogen bonds : bond 0.04379 ( 1134) hydrogen bonds : angle 5.49798 ( 3306) *********************** 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 230 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 138 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7483 (t80) REVERT: A 43 MET cc_start: 0.7350 (ttm) cc_final: 0.6903 (ttm) REVERT: A 97 LYS cc_start: 0.9516 (mttt) cc_final: 0.9295 (ptpp) REVERT: A 134 MET cc_start: 0.8597 (ppp) cc_final: 0.8142 (ppp) REVERT: A 210 ASN cc_start: 0.6665 (OUTLIER) cc_final: 0.6282 (t0) REVERT: A 256 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.7954 (tpp-160) REVERT: A 515 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5291 (tt) REVERT: A 587 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7882 (t) REVERT: B 43 MET cc_start: 0.8548 (mmt) cc_final: 0.8210 (mmt) REVERT: B 109 MET cc_start: 0.8423 (ttm) cc_final: 0.8204 (ttm) REVERT: B 134 MET cc_start: 0.8471 (tmm) cc_final: 0.8127 (tmm) REVERT: B 139 MET cc_start: 0.8604 (tmm) cc_final: 0.8288 (tmm) REVERT: B 317 MET cc_start: 0.8866 (tmm) cc_final: 0.8502 (tmm) REVERT: B 674 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.8565 (m-80) REVERT: C 28 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7449 (t80) REVERT: C 43 MET cc_start: 0.7468 (ttm) cc_final: 0.7004 (ttm) REVERT: C 97 LYS cc_start: 0.9541 (mttt) cc_final: 0.9318 (ptpp) REVERT: C 515 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5279 (tt) REVERT: C 587 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7907 (t) REVERT: D 43 MET cc_start: 0.8539 (mmt) cc_final: 0.8209 (mmt) REVERT: D 134 MET cc_start: 0.8462 (tmm) cc_final: 0.8121 (tmm) REVERT: D 139 MET cc_start: 0.8566 (tmm) cc_final: 0.8262 (tmm) REVERT: D 317 MET cc_start: 0.8859 (tmm) cc_final: 0.8494 (tmm) REVERT: D 674 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8570 (m-80) outliers start: 92 outliers final: 51 residues processed: 213 average time/residue: 0.1318 time to fit residues: 48.3697 Evaluate side-chains 182 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 122 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 131 ILE 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 210 ASN 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 359 VAL Chi-restraints excluded: chain A residue 381 LEU 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 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 306 LEU Chi-restraints excluded: chain B residue 359 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 159 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 195 GLU 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 359 VAL Chi-restraints excluded: chain C residue 381 LEU 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 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 306 LEU Chi-restraints excluded: chain D residue 359 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 261 optimal weight: 0.0770 chunk 128 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN ** 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 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 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 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.062838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.043798 restraints weight = 135695.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.045516 restraints weight = 71723.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.046651 restraints weight = 48155.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.047355 restraints weight = 37301.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.047856 restraints weight = 31798.245| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3164 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= 0.141 Angle : 0.657 16.608 34176 Z= 0.341 Chirality : 0.046 0.213 3884 Planarity : 0.004 0.049 4404 Dihedral : 5.671 55.435 3320 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 3.05 % Allowed : 21.45 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.15), residues: 3100 helix: 1.80 (0.17), residues: 988 sheet: -1.58 (0.20), residues: 632 loop : -2.33 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.009 0.001 TYR D 674 PHE 0.014 0.001 PHE A 193 TRP 0.012 0.001 TRP B 471 HIS 0.006 0.001 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00303 (25268) covalent geometry : angle 0.65672 (34176) hydrogen bonds : bond 0.04280 ( 1134) hydrogen bonds : angle 5.34283 ( 3306) *********************** 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 221 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 135 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7480 (t80) REVERT: A 45 MET cc_start: 0.8999 (tmm) cc_final: 0.8606 (tmm) REVERT: A 97 LYS cc_start: 0.9520 (mttt) cc_final: 0.9306 (ptpp) REVERT: A 134 MET cc_start: 0.8616 (ppp) cc_final: 0.8196 (ppp) REVERT: A 256 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7974 (tpp-160) REVERT: A 515 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5370 (tt) REVERT: A 695 MET cc_start: 0.9202 (mpp) cc_final: 0.8468 (ptp) REVERT: B 43 MET cc_start: 0.8562 (mmt) cc_final: 0.8220 (mmt) REVERT: B 109 MET cc_start: 0.8409 (ttm) cc_final: 0.8193 (ttm) REVERT: B 134 MET cc_start: 0.8494 (tmm) cc_final: 0.8128 (tmm) REVERT: B 139 MET cc_start: 0.8591 (tmm) cc_final: 0.8229 (tmm) REVERT: B 317 MET cc_start: 0.8900 (tmm) cc_final: 0.8515 (tmm) REVERT: B 578 ASN cc_start: 0.9164 (m-40) cc_final: 0.8687 (t0) REVERT: B 674 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.8593 (m-80) REVERT: C 28 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7405 (t80) REVERT: C 97 LYS cc_start: 0.9516 (mttt) cc_final: 0.9303 (ptpp) REVERT: C 515 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5386 (tt) REVERT: C 695 MET cc_start: 0.9181 (mpp) cc_final: 0.8468 (ptp) REVERT: D 43 MET cc_start: 0.8540 (mmt) cc_final: 0.8255 (mmt) REVERT: D 134 MET cc_start: 0.8497 (tmm) cc_final: 0.8129 (tmm) REVERT: D 139 MET cc_start: 0.8558 (tmm) cc_final: 0.8233 (tmm) REVERT: D 317 MET cc_start: 0.8897 (tmm) cc_final: 0.8512 (tmm) REVERT: D 578 ASN cc_start: 0.9159 (m-40) cc_final: 0.8681 (t0) REVERT: D 674 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8595 (m-80) outliers start: 86 outliers final: 53 residues processed: 209 average time/residue: 0.1430 time to fit residues: 51.1922 Evaluate side-chains 183 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 124 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 57 THR 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 195 GLU 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 302 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 381 LEU 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 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 57 THR 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 241 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 381 LEU 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 253 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 359 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 33 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 12 optimal weight: 0.0770 chunk 189 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 253 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- 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 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 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 GLN C 64 ASN C 169 ASN ** 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 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.063193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.044174 restraints weight = 136393.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.045963 restraints weight = 71384.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.047129 restraints weight = 47506.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.047880 restraints weight = 36532.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.048357 restraints weight = 30920.252| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25268 Z= 0.140 Angle : 0.652 16.376 34176 Z= 0.338 Chirality : 0.046 0.198 3884 Planarity : 0.004 0.050 4404 Dihedral : 5.498 54.233 3320 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 2.62 % Allowed : 21.84 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 3100 helix: 1.87 (0.17), residues: 980 sheet: -1.32 (0.20), residues: 640 loop : -2.19 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 256 TYR 0.008 0.001 TYR C 511 PHE 0.020 0.001 PHE D 239 TRP 0.012 0.001 TRP B 471 HIS 0.006 0.001 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00302 (25268) covalent geometry : angle 0.65201 (34176) hydrogen bonds : bond 0.04155 ( 1134) hydrogen bonds : angle 5.21166 ( 3306) *********************** 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 205 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 131 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7440 (t80) REVERT: A 45 MET cc_start: 0.8966 (tmm) cc_final: 0.8568 (tmm) REVERT: A 97 LYS cc_start: 0.9537 (mttt) cc_final: 0.9322 (ptpp) REVERT: A 134 MET cc_start: 0.8651 (ppp) cc_final: 0.8192 (ppp) REVERT: A 157 GLN cc_start: 0.8489 (mm-40) cc_final: 0.7802 (mm110) REVERT: A 236 SER cc_start: 0.6631 (t) cc_final: 0.6112 (m) REVERT: A 256 ARG cc_start: 0.8229 (tpp-160) cc_final: 0.7968 (tpp-160) REVERT: A 515 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5253 (tt) REVERT: B 43 MET cc_start: 0.8555 (mmt) cc_final: 0.8261 (mmt) REVERT: B 109 MET cc_start: 0.8346 (ttm) cc_final: 0.8142 (ttm) REVERT: B 134 MET cc_start: 0.8498 (tmm) cc_final: 0.8209 (tmm) REVERT: B 139 MET cc_start: 0.8504 (tmm) cc_final: 0.8161 (tmm) REVERT: B 317 MET cc_start: 0.8925 (tmm) cc_final: 0.8538 (tmm) REVERT: B 578 ASN cc_start: 0.9200 (m-40) cc_final: 0.8730 (t0) REVERT: B 674 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8596 (m-80) REVERT: C 28 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7448 (t80) REVERT: C 97 LYS cc_start: 0.9541 (mttt) cc_final: 0.9332 (ptpp) REVERT: C 157 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7801 (mm110) REVERT: C 236 SER cc_start: 0.6647 (t) cc_final: 0.6123 (m) REVERT: C 515 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5269 (tt) REVERT: D 43 MET cc_start: 0.8551 (mmt) cc_final: 0.8259 (mmt) REVERT: D 134 MET cc_start: 0.8507 (tmm) cc_final: 0.8217 (tmm) REVERT: D 139 MET cc_start: 0.8567 (tmm) cc_final: 0.8223 (tmm) REVERT: D 317 MET cc_start: 0.8922 (tmm) cc_final: 0.8521 (tmm) REVERT: D 578 ASN cc_start: 0.9209 (m-40) cc_final: 0.8755 (t0) outliers start: 74 outliers final: 54 residues processed: 192 average time/residue: 0.1427 time to fit residues: 47.3365 Evaluate side-chains 188 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 129 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 195 GLU 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 302 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 381 LEU 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 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 234 MET Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 261 THR 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 381 LEU 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 472 LYS Chi-restraints excluded: chain D residue 592 SER 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 195 optimal weight: 9.9990 chunk 241 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 30 optimal weight: 0.0170 chunk 104 optimal weight: 5.9990 chunk 208 optimal weight: 0.0670 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** B 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN ** 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 106 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN D 210 ASN ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.065460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.046571 restraints weight = 131311.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.048471 restraints weight = 66050.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.049715 restraints weight = 43190.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050506 restraints weight = 32865.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.051012 restraints weight = 27647.727| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25268 Z= 0.117 Angle : 0.644 16.614 34176 Z= 0.329 Chirality : 0.045 0.195 3884 Planarity : 0.003 0.058 4404 Dihedral : 5.223 52.158 3320 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 1.95 % Allowed : 22.38 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.15), residues: 3100 helix: 1.94 (0.17), residues: 992 sheet: -1.18 (0.20), residues: 648 loop : -2.14 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 349 TYR 0.009 0.001 TYR B 188 PHE 0.030 0.001 PHE C 254 TRP 0.014 0.001 TRP D 471 HIS 0.006 0.001 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00242 (25268) covalent geometry : angle 0.64395 (34176) hydrogen bonds : bond 0.03863 ( 1134) hydrogen bonds : angle 5.00905 ( 3306) *********************** 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 198 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 143 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7550 (t80) REVERT: A 45 MET cc_start: 0.8969 (tmm) cc_final: 0.8666 (tmm) REVERT: A 97 LYS cc_start: 0.9538 (mttt) cc_final: 0.9335 (ptpp) REVERT: A 134 MET cc_start: 0.8640 (ppp) cc_final: 0.8297 (ppp) REVERT: A 236 SER cc_start: 0.6405 (t) cc_final: 0.5847 (m) REVERT: B 124 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8076 (tt) REVERT: B 134 MET cc_start: 0.8423 (tmm) cc_final: 0.8165 (tmm) REVERT: B 139 MET cc_start: 0.8405 (tmm) cc_final: 0.8042 (tmm) REVERT: B 317 MET cc_start: 0.8844 (tmm) cc_final: 0.8450 (tmm) REVERT: B 578 ASN cc_start: 0.9172 (m-40) cc_final: 0.8791 (t0) REVERT: B 674 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.8623 (m-80) REVERT: C 28 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7518 (t80) REVERT: C 43 MET cc_start: 0.7192 (ttm) cc_final: 0.6811 (ttm) REVERT: C 45 MET cc_start: 0.8913 (tmm) cc_final: 0.8669 (tmm) REVERT: C 236 SER cc_start: 0.6415 (t) cc_final: 0.5858 (m) REVERT: D 43 MET cc_start: 0.8632 (mmt) cc_final: 0.8341 (mmt) REVERT: D 124 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8077 (tt) REVERT: D 134 MET cc_start: 0.8433 (tmm) cc_final: 0.8173 (tmm) REVERT: D 139 MET cc_start: 0.8441 (tmm) cc_final: 0.8081 (tmm) REVERT: D 317 MET cc_start: 0.8844 (tmm) cc_final: 0.8449 (tmm) REVERT: D 578 ASN cc_start: 0.9168 (m-40) cc_final: 0.8786 (t0) outliers start: 55 outliers final: 42 residues processed: 184 average time/residue: 0.1480 time to fit residues: 46.6918 Evaluate side-chains 173 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 163 LEU 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 381 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 112 HIS Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 359 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 28 TYR Chi-restraints excluded: chain C residue 84 ASP 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 234 MET Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 142 ASN 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 207 TYR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 472 LYS 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 121 optimal weight: 7.9990 chunk 245 optimal weight: 3.9990 chunk 286 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 212 optimal weight: 3.9990 chunk 266 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** 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 142 ASN ** B 342 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 106 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.062460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.043363 restraints weight = 137210.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.045101 restraints weight = 72413.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.046217 restraints weight = 48708.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.046942 restraints weight = 37849.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.047385 restraints weight = 32241.267| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25268 Z= 0.210 Angle : 0.711 17.528 34176 Z= 0.365 Chirality : 0.046 0.201 3884 Planarity : 0.004 0.042 4404 Dihedral : 5.493 52.366 3320 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 2.34 % Allowed : 22.06 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 3100 helix: 1.79 (0.17), residues: 962 sheet: -1.27 (0.19), residues: 680 loop : -2.24 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 256 TYR 0.010 0.001 TYR D 127 PHE 0.027 0.001 PHE B 239 TRP 0.010 0.001 TRP B 471 HIS 0.007 0.002 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00460 (25268) covalent geometry : angle 0.71100 (34176) hydrogen bonds : bond 0.04438 ( 1134) hydrogen bonds : angle 5.18305 ( 3306) ********************** 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 186 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 120 time to evaluate : 0.878 Fit side-chains REVERT: A 28 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7318 (t80) REVERT: A 134 MET cc_start: 0.8650 (ppp) cc_final: 0.8192 (ppp) REVERT: A 236 SER cc_start: 0.6587 (t) cc_final: 0.6145 (m) REVERT: A 515 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5294 (tt) REVERT: B 127 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6593 (t80) REVERT: B 134 MET cc_start: 0.8552 (tmm) cc_final: 0.8318 (tmm) REVERT: B 139 MET cc_start: 0.8520 (tmm) cc_final: 0.8192 (tmm) REVERT: B 317 MET cc_start: 0.8954 (tmm) cc_final: 0.8589 (tmm) REVERT: B 578 ASN cc_start: 0.9188 (m-40) cc_final: 0.8771 (t0) REVERT: C 28 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7296 (t80) REVERT: C 157 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7817 (mm-40) REVERT: C 236 SER cc_start: 0.6611 (t) cc_final: 0.6164 (m) REVERT: C 515 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5298 (tt) REVERT: D 43 MET cc_start: 0.8627 (mmt) cc_final: 0.8335 (mmt) REVERT: D 127 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.6589 (t80) REVERT: D 134 MET cc_start: 0.8547 (tmm) cc_final: 0.8318 (tmm) REVERT: D 139 MET cc_start: 0.8577 (tmm) cc_final: 0.8249 (tmm) REVERT: D 317 MET cc_start: 0.8949 (tmm) cc_final: 0.8573 (tmm) REVERT: D 578 ASN cc_start: 0.9187 (m-40) cc_final: 0.8769 (t0) outliers start: 66 outliers final: 52 residues processed: 173 average time/residue: 0.1350 time to fit residues: 40.5911 Evaluate side-chains 175 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 117 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 159 ILE Chi-restraints excluded: chain A residue 163 LEU 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 381 LEU 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 127 TYR Chi-restraints excluded: chain B residue 142 ASN 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 369 ILE Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 592 SER 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 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 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 381 LEU 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 82 LEU Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 142 ASN 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 369 ILE Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 592 SER 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 131 optimal weight: 5.9990 chunk 61 optimal weight: 0.0570 chunk 120 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 233 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 273 optimal weight: 0.0030 chunk 211 optimal weight: 30.0000 overall best weight: 0.9512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** 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 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 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 142 ASN ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.064953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.046178 restraints weight = 134977.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.048103 restraints weight = 67764.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.049335 restraints weight = 44208.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.050134 restraints weight = 33637.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.050664 restraints weight = 28328.805| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3860 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= 0.127 Angle : 0.669 17.051 34176 Z= 0.342 Chirality : 0.046 0.215 3884 Planarity : 0.003 0.037 4404 Dihedral : 5.285 50.498 3320 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 1.84 % Allowed : 22.98 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.15), residues: 3100 helix: 1.75 (0.17), residues: 1004 sheet: -1.13 (0.19), residues: 658 loop : -2.23 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 256 TYR 0.008 0.001 TYR D 28 PHE 0.028 0.001 PHE B 239 TRP 0.014 0.001 TRP D 471 HIS 0.006 0.001 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00262 (25268) covalent geometry : angle 0.66906 (34176) hydrogen bonds : bond 0.04046 ( 1134) hydrogen bonds : angle 5.01603 ( 3306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3948.18 seconds wall clock time: 69 minutes 55.96 seconds (4195.96 seconds total)