Starting phenix.real_space_refine on Sat Jan 25 12:19:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvw_34300/01_2025/8gvw_34300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvw_34300/01_2025/8gvw_34300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gvw_34300/01_2025/8gvw_34300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvw_34300/01_2025/8gvw_34300.map" model { file = "/net/cci-nas-00/data/ceres_data/8gvw_34300/01_2025/8gvw_34300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvw_34300/01_2025/8gvw_34300.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.079 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 116 5.16 5 C 14760 2.51 5 N 3604 2.21 5 O 4000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 22496 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5467 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 646} Chain breaks: 4 Chain: "B" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5467 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 646} Chain breaks: 4 Chain: "C" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5467 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 646} Chain breaks: 4 Chain: "D" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5467 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 646} Chain breaks: 4 Chain: "A" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 193 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 28 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 121 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS A 176 55.311 14.352 74.606 1.00132.73 S ATOM 1162 SG CYS A 178 52.994 12.329 76.873 1.00138.45 S ATOM 1184 SG CYS A 181 52.833 16.060 76.972 1.00127.14 S ATOM 6615 SG CYS B 176 14.361 61.965 74.612 1.00132.17 S ATOM 6629 SG CYS B 178 12.338 64.281 76.880 1.00139.50 S ATOM 6651 SG CYS B 181 16.070 64.443 76.978 1.00128.47 S ATOM 12082 SG CYS C 176 61.976 102.914 74.620 1.00133.10 S ATOM 12096 SG CYS C 178 64.292 104.937 76.888 1.00139.63 S ATOM 12118 SG CYS C 181 64.454 101.205 76.986 1.00128.34 S ATOM 17549 SG CYS D 176 102.925 55.300 74.613 1.00132.40 S ATOM 17563 SG CYS D 178 104.948 52.983 76.880 1.00138.94 S ATOM 17585 SG CYS D 181 101.216 52.821 76.978 1.00127.06 S Time building chain proxies: 13.10, per 1000 atoms: 0.58 Number of scatterers: 22496 At special positions: 0 Unit cell: (118.374, 118.374, 136.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 116 16.00 P 8 15.00 O 4000 8.00 N 3604 7.00 C 14760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 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: 5.97 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 176 " pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 176 " pdb=" ZN C 804 " pdb="ZN ZN C 804 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 176 " pdb=" ZN D 804 " pdb="ZN ZN D 804 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 176 " Number of angles added : 12 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5168 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 0 sheets defined 76.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.666A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 4.033A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.852A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.922A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 426 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.865A pdb=" N ASP A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.829A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 499 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 4.367A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 584 through 588 removed outlier: 3.668A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'A' and resid 615 through 633 removed outlier: 3.783A pdb=" N GLN A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 649 Processing helix chain 'A' and resid 707 through 733 Processing helix chain 'A' and resid 739 through 761 removed outlier: 3.892A pdb=" N PHE A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.666A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 118 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 4.033A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.851A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.922A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 426 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.866A pdb=" N ASP B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.828A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 499 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 4.367A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.669A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 614 Processing helix chain 'B' and resid 615 through 633 removed outlier: 3.783A pdb=" N GLN B 629 " --> pdb=" O ASN B 625 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 649 Processing helix chain 'B' and resid 707 through 733 Processing helix chain 'B' and resid 739 through 761 removed outlier: 3.892A pdb=" N PHE B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.666A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 4.033A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.852A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 271 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 339 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 362 through 385 removed outlier: 3.922A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 426 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 427 through 433 removed outlier: 3.866A pdb=" N ASP C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.829A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 499 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 4.367A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 584 through 588 removed outlier: 3.669A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 614 Processing helix chain 'C' and resid 615 through 633 removed outlier: 3.783A pdb=" N GLN C 629 " --> pdb=" O ASN C 625 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 649 Processing helix chain 'C' and resid 707 through 733 Processing helix chain 'C' and resid 739 through 761 removed outlier: 3.891A pdb=" N PHE C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.666A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 108 through 118 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 164 removed outlier: 4.033A pdb=" N LYS D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.852A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 271 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 339 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 362 through 385 removed outlier: 3.922A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 427 through 433 removed outlier: 3.865A pdb=" N ASP D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.828A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 499 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 4.367A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 584 through 588 removed outlier: 3.669A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 614 Processing helix chain 'D' and resid 615 through 633 removed outlier: 3.783A pdb=" N GLN D 629 " --> pdb=" O ASN D 625 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 649 Processing helix chain 'D' and resid 707 through 733 Processing helix chain 'D' and resid 739 through 761 removed outlier: 3.892A pdb=" N PHE D 743 " --> pdb=" O THR D 739 " (cutoff:3.500A) 1440 hydrogen bonds defined for protein. 4248 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: 6.12 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3577 1.32 - 1.44: 6127 1.44 - 1.57: 13088 1.57 - 1.69: 24 1.69 - 1.81: 188 Bond restraints: 23004 Sorted by residual: bond pdb=" O12 POV A 802 " pdb=" P POV A 802 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" O12 POV D 802 " pdb=" P POV D 802 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" CB PRO C 398 " pdb=" CG PRO C 398 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.56e+00 bond pdb=" O12 POV B 802 " pdb=" P POV B 802 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" O12 POV C 802 " pdb=" P POV C 802 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.55e+00 ... (remaining 22999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 29630 1.91 - 3.82: 1196 3.82 - 5.73: 199 5.73 - 7.65: 55 7.65 - 9.56: 16 Bond angle restraints: 31096 Sorted by residual: angle pdb=" CA PRO C 398 " pdb=" N PRO C 398 " pdb=" CD PRO C 398 " ideal model delta sigma weight residual 112.00 105.71 6.29 1.40e+00 5.10e-01 2.02e+01 angle pdb=" CA PRO A 398 " pdb=" N PRO A 398 " pdb=" CD PRO A 398 " ideal model delta sigma weight residual 112.00 105.74 6.26 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PRO B 398 " pdb=" N PRO B 398 " pdb=" CD PRO B 398 " ideal model delta sigma weight residual 112.00 105.74 6.26 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PRO D 398 " pdb=" N PRO D 398 " pdb=" CD PRO D 398 " ideal model delta sigma weight residual 112.00 105.78 6.22 1.40e+00 5.10e-01 1.97e+01 angle pdb=" CA PHE D 753 " pdb=" CB PHE D 753 " pdb=" CG PHE D 753 " ideal model delta sigma weight residual 113.80 117.54 -3.74 1.00e+00 1.00e+00 1.40e+01 ... (remaining 31091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 13720 34.94 - 69.87: 268 69.87 - 104.81: 28 104.81 - 139.74: 20 139.74 - 174.68: 4 Dihedral angle restraints: 14040 sinusoidal: 6096 harmonic: 7944 Sorted by residual: dihedral pdb=" C26 YZY C 806 " pdb=" C27 YZY C 806 " pdb=" C28 YZY C 806 " pdb=" C29 YZY C 806 " ideal model delta sinusoidal sigma weight residual 119.11 -55.57 174.68 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 807 " pdb=" C27 YZY A 807 " pdb=" C28 YZY A 807 " pdb=" C29 YZY A 807 " ideal model delta sinusoidal sigma weight residual 119.11 -55.56 174.67 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 806 " pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sinusoidal sigma weight residual 119.11 -55.53 174.64 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 14037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2724 0.052 - 0.105: 608 0.105 - 0.157: 120 0.157 - 0.209: 20 0.209 - 0.262: 4 Chirality restraints: 3476 Sorted by residual: chirality pdb=" CB VAL C 590 " pdb=" CA VAL C 590 " pdb=" CG1 VAL C 590 " pdb=" CG2 VAL C 590 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL D 590 " pdb=" CA VAL D 590 " pdb=" CG1 VAL D 590 " pdb=" CG2 VAL D 590 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL A 590 " pdb=" CA VAL A 590 " pdb=" CG1 VAL A 590 " pdb=" CG2 VAL A 590 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 3473 not shown) Planarity restraints: 3828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 397 " 0.049 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO B 398 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 398 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 398 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 397 " 0.049 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO A 398 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 398 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 398 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 397 " 0.049 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO C 398 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 398 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 398 " 0.039 5.00e-02 4.00e+02 ... (remaining 3825 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3938 2.77 - 3.30: 21644 3.30 - 3.83: 36931 3.83 - 4.37: 42327 4.37 - 4.90: 74193 Nonbonded interactions: 179033 Sorted by model distance: nonbonded pdb=" OH TYR C 374 " pdb=" O SER C 489 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 374 " pdb=" O SER A 489 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR D 374 " pdb=" O SER D 489 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR B 374 " pdb=" O SER B 489 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASP C 215 " pdb=" OH TYR C 713 " model vdw 2.288 3.040 ... (remaining 179028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 761 or resid 801 through 805)) selection = (chain 'B' and (resid 17 through 761 or resid 801 through 805)) selection = (chain 'C' and (resid 17 through 761 or resid 801 through 805)) 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 49.800 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 0.128 23004 Z= 0.361 Angle : 0.894 9.558 31096 Z= 0.464 Chirality : 0.047 0.262 3476 Planarity : 0.007 0.081 3828 Dihedral : 15.334 174.677 8860 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.17 % Allowed : 0.67 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 2644 helix: 0.35 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : -0.71 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 410 HIS 0.003 0.001 HIS B 735 PHE 0.038 0.002 PHE B 753 TYR 0.032 0.002 TYR C 724 ARG 0.007 0.001 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 515 time to evaluate : 2.462 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8396 (pttm) cc_final: 0.7659 (pttm) REVERT: A 48 VAL cc_start: 0.9046 (t) cc_final: 0.8833 (p) REVERT: A 479 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 598 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8146 (mm-30) REVERT: A 628 TYR cc_start: 0.8945 (t80) cc_final: 0.8675 (t80) REVERT: A 728 MET cc_start: 0.7780 (ttp) cc_final: 0.7564 (ttp) REVERT: B 42 LYS cc_start: 0.8404 (pttm) cc_final: 0.7680 (pttm) REVERT: B 48 VAL cc_start: 0.9061 (t) cc_final: 0.8831 (p) REVERT: B 598 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8146 (mm-30) REVERT: B 628 TYR cc_start: 0.8936 (t80) cc_final: 0.8667 (t80) REVERT: C 42 LYS cc_start: 0.8408 (pttm) cc_final: 0.7639 (pttm) REVERT: C 48 VAL cc_start: 0.9086 (t) cc_final: 0.8873 (p) REVERT: C 598 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8112 (mm-30) REVERT: C 628 TYR cc_start: 0.8943 (t80) cc_final: 0.8627 (t80) REVERT: C 728 MET cc_start: 0.7835 (ttp) cc_final: 0.7612 (ttp) REVERT: D 42 LYS cc_start: 0.8408 (pttm) cc_final: 0.7649 (pttm) REVERT: D 541 TYR cc_start: 0.7959 (m-10) cc_final: 0.7759 (m-10) REVERT: D 728 MET cc_start: 0.7812 (ttp) cc_final: 0.7597 (ttp) outliers start: 4 outliers final: 0 residues processed: 515 average time/residue: 0.3099 time to fit residues: 257.7482 Evaluate side-chains 384 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 0.0670 chunk 210 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 127 optimal weight: 0.0470 chunk 156 optimal weight: 3.9990 chunk 243 optimal weight: 0.4980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 GLN D 21 GLN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.163712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123329 restraints weight = 29103.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124471 restraints weight = 18847.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125793 restraints weight = 13289.561| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23004 Z= 0.220 Angle : 0.564 6.702 31096 Z= 0.291 Chirality : 0.039 0.161 3476 Planarity : 0.004 0.047 3828 Dihedral : 12.388 116.357 3576 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.33 % Allowed : 11.06 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.16), residues: 2644 helix: 1.36 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.49 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 315 HIS 0.003 0.001 HIS D 712 PHE 0.014 0.001 PHE C 540 TYR 0.015 0.001 TYR C 118 ARG 0.004 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 418 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 CYS cc_start: 0.8220 (p) cc_final: 0.7908 (p) REVERT: A 337 ILE cc_start: 0.8981 (mm) cc_final: 0.8737 (mt) REVERT: A 479 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7191 (mm-30) REVERT: A 541 TYR cc_start: 0.7936 (m-10) cc_final: 0.7582 (m-10) REVERT: A 728 MET cc_start: 0.7694 (ttp) cc_final: 0.7481 (ttp) REVERT: B 65 CYS cc_start: 0.8344 (p) cc_final: 0.8048 (p) REVERT: B 114 LEU cc_start: 0.8954 (mm) cc_final: 0.8597 (mm) REVERT: B 337 ILE cc_start: 0.8987 (mm) cc_final: 0.8752 (mt) REVERT: B 541 TYR cc_start: 0.7930 (m-10) cc_final: 0.7582 (m-10) REVERT: C 65 CYS cc_start: 0.8349 (p) cc_final: 0.8041 (p) REVERT: C 114 LEU cc_start: 0.8966 (mm) cc_final: 0.8613 (mm) REVERT: C 337 ILE cc_start: 0.8977 (mm) cc_final: 0.8732 (mt) REVERT: C 340 LEU cc_start: 0.9285 (mt) cc_final: 0.9071 (mp) REVERT: C 541 TYR cc_start: 0.7918 (m-10) cc_final: 0.7561 (m-10) REVERT: C 728 MET cc_start: 0.7714 (ttp) cc_final: 0.7501 (ttp) REVERT: D 65 CYS cc_start: 0.8396 (p) cc_final: 0.8075 (p) REVERT: D 114 LEU cc_start: 0.8978 (mm) cc_final: 0.8658 (mm) REVERT: D 337 ILE cc_start: 0.8967 (mm) cc_final: 0.8725 (mt) REVERT: D 340 LEU cc_start: 0.9251 (mt) cc_final: 0.9032 (mp) REVERT: D 541 TYR cc_start: 0.8133 (m-10) cc_final: 0.7708 (m-10) REVERT: D 728 MET cc_start: 0.7708 (ttp) cc_final: 0.7498 (ttp) REVERT: D 741 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8229 (mp0) outliers start: 8 outliers final: 8 residues processed: 420 average time/residue: 0.3103 time to fit residues: 212.7650 Evaluate side-chains 372 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 364 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 383 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 53 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 245 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 251 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 309 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** D 625 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 = 0.3829 r_free = 0.3829 target = 0.157439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117821 restraints weight = 29150.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119022 restraints weight = 18250.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119766 restraints weight = 15708.638| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23004 Z= 0.343 Angle : 0.619 7.763 31096 Z= 0.317 Chirality : 0.042 0.193 3476 Planarity : 0.004 0.045 3828 Dihedral : 11.473 123.285 3576 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.71 % Allowed : 13.36 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.16), residues: 2644 helix: 1.61 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.45 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 315 HIS 0.004 0.001 HIS B 151 PHE 0.014 0.002 PHE D 540 TYR 0.017 0.002 TYR C 524 ARG 0.003 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 402 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ILE cc_start: 0.8586 (mm) cc_final: 0.8331 (mm) REVERT: A 479 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7441 (mm-30) REVERT: A 541 TYR cc_start: 0.8124 (m-10) cc_final: 0.7775 (m-10) REVERT: A 728 MET cc_start: 0.7774 (ttp) cc_final: 0.7555 (ttp) REVERT: B 114 LEU cc_start: 0.9046 (mm) cc_final: 0.8712 (mm) REVERT: B 541 TYR cc_start: 0.8115 (m-10) cc_final: 0.7768 (m-10) REVERT: C 114 LEU cc_start: 0.9050 (mm) cc_final: 0.8714 (mm) REVERT: C 337 ILE cc_start: 0.9048 (mm) cc_final: 0.8818 (mp) REVERT: C 541 TYR cc_start: 0.8120 (m-10) cc_final: 0.7773 (m-10) REVERT: C 728 MET cc_start: 0.7775 (ttp) cc_final: 0.7557 (ttp) REVERT: D 114 LEU cc_start: 0.9057 (mm) cc_final: 0.8736 (mm) REVERT: D 157 ILE cc_start: 0.8553 (mm) cc_final: 0.8284 (mm) REVERT: D 337 ILE cc_start: 0.9044 (mm) cc_final: 0.8811 (mp) REVERT: D 541 TYR cc_start: 0.8124 (m-10) cc_final: 0.7632 (m-10) REVERT: D 728 MET cc_start: 0.7763 (ttp) cc_final: 0.7534 (ttp) outliers start: 41 outliers final: 36 residues processed: 425 average time/residue: 0.3101 time to fit residues: 213.9528 Evaluate side-chains 401 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 365 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 252 optimal weight: 0.9990 chunk 187 optimal weight: 0.5980 chunk 179 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 21 GLN B 609 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN C 21 GLN C 609 ASN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 609 ASN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.159812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121249 restraints weight = 29486.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119786 restraints weight = 19290.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121621 restraints weight = 18359.051| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23004 Z= 0.201 Angle : 0.540 8.674 31096 Z= 0.272 Chirality : 0.039 0.161 3476 Planarity : 0.004 0.047 3828 Dihedral : 11.159 121.536 3576 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.46 % Allowed : 15.19 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.16), residues: 2644 helix: 1.88 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.43 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 315 HIS 0.003 0.001 HIS C 735 PHE 0.014 0.001 PHE C 341 TYR 0.017 0.001 TYR B 118 ARG 0.002 0.000 ARG B 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 390 time to evaluate : 2.516 Fit side-chains REVERT: A 236 GLU cc_start: 0.7650 (pm20) cc_final: 0.7413 (mp0) REVERT: A 479 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 539 TYR cc_start: 0.9154 (m-80) cc_final: 0.8907 (m-80) REVERT: A 541 TYR cc_start: 0.8177 (m-10) cc_final: 0.7904 (m-10) REVERT: A 728 MET cc_start: 0.7675 (ttp) cc_final: 0.7426 (ttm) REVERT: A 744 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7166 (mttp) REVERT: B 236 GLU cc_start: 0.7617 (pm20) cc_final: 0.7408 (mp0) REVERT: B 337 ILE cc_start: 0.9029 (mm) cc_final: 0.8825 (mt) REVERT: B 479 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7429 (mm-30) REVERT: B 539 TYR cc_start: 0.9156 (m-80) cc_final: 0.8911 (m-80) REVERT: B 541 TYR cc_start: 0.8183 (m-10) cc_final: 0.7910 (m-10) REVERT: C 236 GLU cc_start: 0.7591 (pm20) cc_final: 0.7389 (mp0) REVERT: C 337 ILE cc_start: 0.8992 (mm) cc_final: 0.8756 (mt) REVERT: C 479 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7428 (mm-30) REVERT: C 539 TYR cc_start: 0.9158 (m-80) cc_final: 0.8913 (m-80) REVERT: C 541 TYR cc_start: 0.8196 (m-10) cc_final: 0.7925 (m-10) REVERT: C 728 MET cc_start: 0.7661 (ttp) cc_final: 0.7410 (ttm) REVERT: D 21 GLN cc_start: 0.6651 (mm110) cc_final: 0.6423 (mp10) REVERT: D 114 LEU cc_start: 0.9065 (mm) cc_final: 0.8758 (mm) REVERT: D 147 MET cc_start: 0.8035 (mtp) cc_final: 0.7733 (mtp) REVERT: D 157 ILE cc_start: 0.8623 (mm) cc_final: 0.8293 (mm) REVERT: D 337 ILE cc_start: 0.8996 (mm) cc_final: 0.8765 (mt) REVERT: D 479 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7432 (mm-30) REVERT: D 539 TYR cc_start: 0.9160 (m-80) cc_final: 0.8923 (m-80) REVERT: D 541 TYR cc_start: 0.8204 (m-10) cc_final: 0.7629 (m-10) REVERT: D 728 MET cc_start: 0.7684 (ttp) cc_final: 0.7448 (ttp) outliers start: 35 outliers final: 15 residues processed: 413 average time/residue: 0.3470 time to fit residues: 228.7696 Evaluate side-chains 375 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 359 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 744 LYS Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.2201 > 50: distance: 4 - 7: 35.013 distance: 8 - 9: 37.205 distance: 8 - 11: 11.893 distance: 9 - 10: 27.565 distance: 9 - 16: 32.967 distance: 11 - 12: 10.252 distance: 13 - 14: 15.332 distance: 13 - 15: 27.042 distance: 16 - 17: 22.633 distance: 17 - 18: 45.922 distance: 17 - 20: 21.214 distance: 18 - 19: 11.539 distance: 18 - 23: 34.162 distance: 20 - 21: 41.389 distance: 20 - 22: 4.563 distance: 23 - 24: 36.695 distance: 24 - 25: 41.759 distance: 24 - 27: 9.813 distance: 25 - 26: 26.710 distance: 25 - 32: 24.943 distance: 27 - 28: 22.295 distance: 28 - 29: 43.846 distance: 29 - 30: 12.414 distance: 29 - 31: 44.751 distance: 32 - 33: 16.626 distance: 33 - 34: 24.821 distance: 33 - 36: 48.622 distance: 34 - 35: 18.903 distance: 34 - 40: 21.827 distance: 36 - 37: 42.395 distance: 37 - 38: 40.018 distance: 37 - 39: 42.944 distance: 40 - 41: 11.095 distance: 41 - 42: 10.064 distance: 41 - 44: 13.146 distance: 42 - 43: 14.713 distance: 42 - 46: 11.591 distance: 43 - 69: 22.130 distance: 44 - 45: 22.430 distance: 46 - 47: 8.685 distance: 47 - 48: 16.042 distance: 47 - 50: 4.257 distance: 48 - 49: 20.583 distance: 48 - 51: 4.681 distance: 49 - 78: 8.736 distance: 51 - 52: 9.448 distance: 52 - 53: 4.494 distance: 52 - 55: 3.851 distance: 53 - 54: 9.937 distance: 53 - 60: 13.040 distance: 54 - 83: 8.542 distance: 56 - 57: 8.397 distance: 57 - 58: 8.021 distance: 57 - 59: 8.900 distance: 60 - 61: 5.476 distance: 61 - 62: 13.425 distance: 61 - 64: 10.820 distance: 62 - 63: 15.175 distance: 62 - 69: 9.378 distance: 63 - 90: 13.706 distance: 64 - 65: 3.257 distance: 65 - 66: 16.554 distance: 66 - 67: 11.489 distance: 66 - 68: 8.187 distance: 69 - 70: 9.821 distance: 70 - 71: 3.423 distance: 70 - 73: 9.592 distance: 71 - 72: 5.849 distance: 71 - 78: 26.609 distance: 72 - 97: 27.246 distance: 73 - 74: 4.727 distance: 74 - 75: 7.160 distance: 75 - 76: 16.348 distance: 76 - 77: 17.899 distance: 78 - 79: 30.297 distance: 79 - 80: 34.413 distance: 79 - 82: 11.710 distance: 80 - 81: 24.827 distance: 80 - 83: 20.892 distance: 81 - 104: 31.202