Starting phenix.real_space_refine on Sat Jul 4 20:32:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gvw_34300/07_2026/8gvw_34300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvw_34300/07_2026/8gvw_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gvw_34300/07_2026/8gvw_34300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvw_34300/07_2026/8gvw_34300.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gvw_34300/07_2026/8gvw_34300.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gvw_34300/07_2026/8gvw_34300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gvw_34300/07_2026/8gvw_34300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvw_34300/07_2026/8gvw_34300.map" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.079 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 5.24, per 1000 atoms: 0.23 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: 2.13 Conformation dependent library (CDL) restraints added in 1.1 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: 0.66 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: 4.47 Time building geometry restraints manager: 2.80 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: 13432 34.94 - 69.87: 252 69.87 - 104.81: 28 104.81 - 139.74: 20 139.74 - 174.68: 4 Dihedral angle restraints: 13736 sinusoidal: 5792 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 13733 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 805) selection = (chain 'B' and resid 17 through 805) selection = (chain 'C' and resid 17 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: 0.010 Normalize map: mean=0, sd=1: 4.620 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.810 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 23024 Z= 0.253 Angle : 0.896 9.558 31116 Z= 0.465 Chirality : 0.047 0.262 3476 Planarity : 0.007 0.081 3828 Dihedral : 15.355 174.677 8556 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.59 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 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: 0.01 (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 ARG 0.007 0.001 ARG C 464 TYR 0.032 0.002 TYR C 724 PHE 0.038 0.002 PHE B 753 TRP 0.020 0.002 TRP C 410 HIS 0.003 0.001 HIS B 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.25 (23004) covalent geometry : angle 0.89412 / 0.46 (31096) SS BOND : bond 0.00248 / 0.12 ( 4) SS BOND : angle 1.99070 / 1.41 ( 8) hydrogen bonds : bond 0.09118 / 6.00 ( 1440) hydrogen bonds : angle 4.45732 / 3.15 ( 4248) metal coordination : bond 0.00965 / 0.89 ( 16) metal coordination : angle 2.54639 / 1.42 ( 12) *********************** 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 : 0.838 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: 0.8414 (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: 0.7779 (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: 0.1432 time to fit residues: 120.8097 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 : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 0.0770 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 625 ASN B 625 ASN C 625 ASN D 21 GLN D 625 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.165567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124405 restraints weight = 29301.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126589 restraints weight = 16285.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127932 restraints weight = 11677.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128574 restraints weight = 10178.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128576 restraints weight = 9425.936| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23024 Z= 0.128 Angle : 0.552 6.736 31116 Z= 0.285 Chirality : 0.039 0.161 3476 Planarity : 0.004 0.048 3828 Dihedral : 12.501 121.179 3272 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.71 % Allowed : 10.23 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.16), residues: 2644 helix: 1.34 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.50 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 263 TYR 0.015 0.001 TYR C 118 PHE 0.014 0.001 PHE C 540 TRP 0.011 0.001 TRP A 315 HIS 0.004 0.001 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (23004) covalent geometry : angle 0.55071 / 0.28 (31096) SS BOND : bond 0.00164 / 0.08 ( 4) SS BOND : angle 0.38939 / 0.28 ( 8) hydrogen bonds : bond 0.04095 / 2.70 ( 1440) hydrogen bonds : angle 3.64244 / 2.59 ( 4248) metal coordination : bond 0.00367 / 0.32 ( 16) metal coordination : angle 1.76939 / 0.97 ( 12) *********************** 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 431 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 414 time to evaluate : 0.837 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 114 LEU cc_start: 0.8914 (mm) cc_final: 0.8546 (mm) REVERT: A 337 ILE cc_start: 0.8922 (mm) cc_final: 0.8669 (mt) REVERT: A 340 LEU cc_start: 0.9291 (mt) cc_final: 0.9083 (mp) REVERT: A 479 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7181 (mm-30) REVERT: A 541 TYR cc_start: 0.7870 (m-10) cc_final: 0.7519 (m-10) REVERT: A 741 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8248 (mp0) REVERT: B 65 CYS cc_start: 0.8498 (p) cc_final: 0.8185 (p) REVERT: B 337 ILE cc_start: 0.8941 (mm) cc_final: 0.8694 (mt) REVERT: B 541 TYR cc_start: 0.7859 (m-10) cc_final: 0.7515 (m-10) REVERT: C 65 CYS cc_start: 0.8501 (p) cc_final: 0.8175 (p) REVERT: C 114 LEU cc_start: 0.8933 (mm) cc_final: 0.8580 (mm) REVERT: C 337 ILE cc_start: 0.8917 (mm) cc_final: 0.8661 (mt) REVERT: C 340 LEU cc_start: 0.9293 (mt) cc_final: 0.9078 (mp) REVERT: C 541 TYR cc_start: 0.7868 (m-10) cc_final: 0.7515 (m-10) REVERT: C 728 MET cc_start: 0.7701 (ttp) cc_final: 0.7494 (ttp) REVERT: D 114 LEU cc_start: 0.8928 (mm) cc_final: 0.8565 (mm) REVERT: D 337 ILE cc_start: 0.8913 (mm) cc_final: 0.8655 (mt) REVERT: D 340 LEU cc_start: 0.9262 (mt) cc_final: 0.9040 (mp) REVERT: D 427 PHE cc_start: 0.7935 (t80) cc_final: 0.7623 (t80) REVERT: D 541 TYR cc_start: 0.8073 (m-10) cc_final: 0.7683 (m-10) REVERT: D 728 MET cc_start: 0.7693 (ttp) cc_final: 0.7488 (ttp) REVERT: D 741 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8237 (mp0) outliers start: 17 outliers final: 11 residues processed: 424 average time/residue: 0.1212 time to fit residues: 85.9930 Evaluate side-chains 371 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 360 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 LEU 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 197 LEU 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 50 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 256 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 192 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.163172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123972 restraints weight = 29150.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123688 restraints weight = 17935.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124948 restraints weight = 16931.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125448 restraints weight = 12618.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125780 restraints weight = 11864.405| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23024 Z= 0.136 Angle : 0.529 8.256 31116 Z= 0.272 Chirality : 0.039 0.158 3476 Planarity : 0.004 0.045 3828 Dihedral : 11.183 115.353 3272 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.13 % Allowed : 12.48 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.16), residues: 2644 helix: 1.74 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.46 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 512 TYR 0.018 0.001 TYR D 118 PHE 0.013 0.001 PHE D 540 TRP 0.012 0.001 TRP D 315 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (23004) covalent geometry : angle 0.52819 / 0.27 (31096) SS BOND : bond 0.00148 / 0.07 ( 4) SS BOND : angle 0.24107 / 0.16 ( 8) hydrogen bonds : bond 0.03973 / 2.63 ( 1440) hydrogen bonds : angle 3.48710 / 2.48 ( 4248) metal coordination : bond 0.00249 / 0.18 ( 16) metal coordination : angle 1.55481 / 0.86 ( 12) *********************** 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 409 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 382 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 114 LEU cc_start: 0.9005 (mm) cc_final: 0.8676 (mm) REVERT: A 337 ILE cc_start: 0.8942 (mm) cc_final: 0.8694 (mt) REVERT: A 479 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7301 (mm-30) REVERT: A 539 TYR cc_start: 0.9198 (m-80) cc_final: 0.8822 (m-80) REVERT: A 541 TYR cc_start: 0.8007 (m-10) cc_final: 0.7505 (m-10) REVERT: B 114 LEU cc_start: 0.9002 (mm) cc_final: 0.8676 (mm) REVERT: B 539 TYR cc_start: 0.9188 (m-80) cc_final: 0.8816 (m-80) REVERT: B 541 TYR cc_start: 0.7995 (m-10) cc_final: 0.7494 (m-10) REVERT: C 114 LEU cc_start: 0.9011 (mm) cc_final: 0.8686 (mm) REVERT: C 337 ILE cc_start: 0.8933 (mm) cc_final: 0.8678 (mt) REVERT: C 539 TYR cc_start: 0.9197 (m-80) cc_final: 0.8834 (m-80) REVERT: C 541 TYR cc_start: 0.8005 (m-10) cc_final: 0.7505 (m-10) REVERT: C 744 LYS cc_start: 0.7156 (mttt) cc_final: 0.6774 (mttp) REVERT: D 65 CYS cc_start: 0.7993 (p) cc_final: 0.7515 (p) REVERT: D 114 LEU cc_start: 0.8970 (mm) cc_final: 0.8646 (mm) REVERT: D 337 ILE cc_start: 0.8928 (mm) cc_final: 0.8672 (mt) REVERT: D 539 TYR cc_start: 0.9195 (m-80) cc_final: 0.8856 (m-80) REVERT: D 541 TYR cc_start: 0.8155 (m-10) cc_final: 0.7780 (m-10) outliers start: 27 outliers final: 20 residues processed: 399 average time/residue: 0.1346 time to fit residues: 88.1993 Evaluate side-chains 366 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 346 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR 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 567 THR Chi-restraints excluded: chain C residue 725 VAL 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 567 THR 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 116 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 68 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.162059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123657 restraints weight = 29429.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122736 restraints weight = 19525.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123932 restraints weight = 20960.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125639 restraints weight = 13989.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125966 restraints weight = 12379.115| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23024 Z= 0.141 Angle : 0.532 9.612 31116 Z= 0.269 Chirality : 0.039 0.174 3476 Planarity : 0.004 0.047 3828 Dihedral : 10.899 118.216 3272 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.38 % Allowed : 13.90 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.16), residues: 2644 helix: 1.91 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.45 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 512 TYR 0.015 0.001 TYR C 524 PHE 0.013 0.001 PHE B 341 TRP 0.011 0.001 TRP A 315 HIS 0.003 0.001 HIS C 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (23004) covalent geometry : angle 0.53168 / 0.27 (31096) SS BOND : bond 0.00185 / 0.09 ( 4) SS BOND : angle 0.19928 / 0.13 ( 8) hydrogen bonds : bond 0.03904 / 2.59 ( 1440) hydrogen bonds : angle 3.44783 / 2.45 ( 4248) metal coordination : bond 0.00212 / 0.15 ( 16) metal coordination : angle 1.33807 / 0.75 ( 12) *********************** 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 408 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 375 time to evaluate : 0.868 Fit side-chains REVERT: A 337 ILE cc_start: 0.8978 (mm) cc_final: 0.8730 (mt) REVERT: A 479 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7331 (mm-30) REVERT: A 539 TYR cc_start: 0.9178 (m-80) cc_final: 0.8870 (m-80) REVERT: A 541 TYR cc_start: 0.8085 (m-10) cc_final: 0.7565 (m-10) REVERT: B 479 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 539 TYR cc_start: 0.9169 (m-80) cc_final: 0.8851 (m-80) REVERT: B 541 TYR cc_start: 0.8080 (m-10) cc_final: 0.7557 (m-10) REVERT: C 147 MET cc_start: 0.7977 (mtp) cc_final: 0.7731 (mtp) REVERT: C 337 ILE cc_start: 0.8965 (mm) cc_final: 0.8716 (mt) REVERT: C 479 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7177 (mm-30) REVERT: C 539 TYR cc_start: 0.9178 (m-80) cc_final: 0.8863 (m-80) REVERT: C 541 TYR cc_start: 0.8085 (m-10) cc_final: 0.7564 (m-10) REVERT: D 337 ILE cc_start: 0.8969 (mm) cc_final: 0.8716 (mt) REVERT: D 479 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7197 (mm-30) REVERT: D 539 TYR cc_start: 0.9180 (m-80) cc_final: 0.8876 (m-80) REVERT: D 541 TYR cc_start: 0.8116 (m-10) cc_final: 0.7755 (m-10) outliers start: 33 outliers final: 27 residues processed: 399 average time/residue: 0.1312 time to fit residues: 85.8248 Evaluate side-chains 369 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 342 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR 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 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 341 PHE 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 725 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 17 optimal weight: 0.1980 chunk 117 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 257 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 245 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 GLN ** D 625 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 = 0.3874 r_free = 0.3874 target = 0.161775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123476 restraints weight = 29181.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122049 restraints weight = 19790.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124114 restraints weight = 19377.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124508 restraints weight = 13520.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128021 restraints weight = 12491.675| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23024 Z= 0.124 Angle : 0.524 8.881 31116 Z= 0.264 Chirality : 0.039 0.188 3476 Planarity : 0.004 0.049 3828 Dihedral : 10.809 118.653 3272 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.71 % Allowed : 14.44 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.16), residues: 2644 helix: 2.02 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.47 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 754 TYR 0.015 0.001 TYR B 524 PHE 0.013 0.001 PHE B 341 TRP 0.010 0.001 TRP B 315 HIS 0.002 0.000 HIS D 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (23004) covalent geometry : angle 0.52379 / 0.26 (31096) SS BOND : bond 0.00136 / 0.07 ( 4) SS BOND : angle 0.12970 / 0.07 ( 8) hydrogen bonds : bond 0.03768 / 2.50 ( 1440) hydrogen bonds : angle 3.41063 / 2.43 ( 4248) metal coordination : bond 0.00196 / 0.15 ( 16) metal coordination : angle 1.04944 / 0.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 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 421 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 380 time to evaluate : 0.857 Fit side-chains REVERT: A 66 MET cc_start: 0.8863 (mmm) cc_final: 0.8634 (mmm) REVERT: A 157 ILE cc_start: 0.8447 (mm) cc_final: 0.8211 (mm) REVERT: A 337 ILE cc_start: 0.8975 (mm) cc_final: 0.8724 (mt) REVERT: A 539 TYR cc_start: 0.9142 (m-80) cc_final: 0.8920 (m-80) REVERT: A 541 TYR cc_start: 0.8141 (m-10) cc_final: 0.7678 (m-10) REVERT: A 744 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7214 (mttp) REVERT: B 66 MET cc_start: 0.8824 (mmm) cc_final: 0.8585 (mmm) REVERT: B 157 ILE cc_start: 0.8468 (mm) cc_final: 0.8246 (mm) REVERT: B 539 TYR cc_start: 0.9131 (m-80) cc_final: 0.8892 (m-80) REVERT: B 541 TYR cc_start: 0.8126 (m-10) cc_final: 0.7660 (m-10) REVERT: C 147 MET cc_start: 0.7992 (mtp) cc_final: 0.7726 (mtp) REVERT: C 157 ILE cc_start: 0.8426 (mm) cc_final: 0.8185 (mm) REVERT: C 337 ILE cc_start: 0.8982 (mm) cc_final: 0.8744 (mt) REVERT: C 539 TYR cc_start: 0.9144 (m-80) cc_final: 0.8913 (m-80) REVERT: C 541 TYR cc_start: 0.8145 (m-10) cc_final: 0.7681 (m-10) REVERT: D 21 GLN cc_start: 0.6656 (mm110) cc_final: 0.6424 (mp10) REVERT: D 66 MET cc_start: 0.8850 (mmm) cc_final: 0.8597 (mmm) REVERT: D 337 ILE cc_start: 0.8972 (mm) cc_final: 0.8728 (mt) REVERT: D 539 TYR cc_start: 0.9144 (m-80) cc_final: 0.8925 (m-80) outliers start: 41 outliers final: 34 residues processed: 417 average time/residue: 0.1306 time to fit residues: 89.4711 Evaluate side-chains 387 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 352 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 744 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 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 C residue 567 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 51 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 249 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 172 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 609 ASN ** 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 = 0.3872 r_free = 0.3872 target = 0.161301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123042 restraints weight = 29428.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121874 restraints weight = 20287.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123712 restraints weight = 18657.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124898 restraints weight = 12741.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125174 restraints weight = 11721.692| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23024 Z= 0.123 Angle : 0.512 9.234 31116 Z= 0.259 Chirality : 0.038 0.179 3476 Planarity : 0.004 0.049 3828 Dihedral : 10.763 119.307 3272 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.88 % Allowed : 15.36 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.16), residues: 2644 helix: 2.09 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.45 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 754 TYR 0.015 0.001 TYR C 524 PHE 0.013 0.001 PHE C 341 TRP 0.010 0.001 TRP C 315 HIS 0.002 0.000 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (23004) covalent geometry : angle 0.51154 / 0.26 (31096) SS BOND : bond 0.00140 / 0.07 ( 4) SS BOND : angle 0.12975 / 0.07 ( 8) hydrogen bonds : bond 0.03733 / 2.48 ( 1440) hydrogen bonds : angle 3.37815 / 2.40 ( 4248) metal coordination : bond 0.00215 / 0.18 ( 16) metal coordination : angle 0.98815 / 0.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 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: 45 poor density : 380 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8799 (mmm) cc_final: 0.8548 (mmm) REVERT: A 114 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8926 (mm) REVERT: A 147 MET cc_start: 0.7957 (mtp) cc_final: 0.7703 (mtp) REVERT: A 337 ILE cc_start: 0.9026 (mm) cc_final: 0.8818 (mt) REVERT: A 479 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7196 (mm-30) REVERT: A 541 TYR cc_start: 0.8035 (m-10) cc_final: 0.7768 (m-10) REVERT: B 66 MET cc_start: 0.8801 (mmm) cc_final: 0.8559 (mmm) REVERT: B 147 MET cc_start: 0.7981 (mtp) cc_final: 0.7741 (mtp) REVERT: B 541 TYR cc_start: 0.8030 (m-10) cc_final: 0.7762 (m-10) REVERT: C 66 MET cc_start: 0.8798 (mmm) cc_final: 0.8553 (mmm) REVERT: C 337 ILE cc_start: 0.9017 (mm) cc_final: 0.8780 (mt) REVERT: C 541 TYR cc_start: 0.8025 (m-10) cc_final: 0.7760 (m-10) REVERT: D 21 GLN cc_start: 0.6747 (mm110) cc_final: 0.6537 (mp10) REVERT: D 66 MET cc_start: 0.8806 (mmm) cc_final: 0.8536 (mmm) REVERT: D 114 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8939 (mm) REVERT: D 337 ILE cc_start: 0.8995 (mm) cc_final: 0.8754 (mt) REVERT: D 541 TYR cc_start: 0.8150 (m-10) cc_final: 0.7527 (m-10) outliers start: 45 outliers final: 30 residues processed: 411 average time/residue: 0.1365 time to fit residues: 91.0565 Evaluate side-chains 386 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 354 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 LEU 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 C residue 567 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 147 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.160165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121331 restraints weight = 29589.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120089 restraints weight = 19801.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.121828 restraints weight = 18151.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122552 restraints weight = 13273.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122834 restraints weight = 12320.440| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23024 Z= 0.146 Angle : 0.538 7.951 31116 Z= 0.274 Chirality : 0.039 0.184 3476 Planarity : 0.004 0.049 3828 Dihedral : 10.841 123.245 3272 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.92 % Allowed : 16.19 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.16), residues: 2644 helix: 2.11 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.37 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 754 TYR 0.019 0.001 TYR C 118 PHE 0.013 0.001 PHE C 341 TRP 0.012 0.001 TRP B 315 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (23004) covalent geometry : angle 0.53781 / 0.27 (31096) SS BOND : bond 0.00159 / 0.08 ( 4) SS BOND : angle 0.25736 / 0.15 ( 8) hydrogen bonds : bond 0.03875 / 2.57 ( 1440) hydrogen bonds : angle 3.42412 / 2.43 ( 4248) metal coordination : bond 0.00216 / 0.19 ( 16) metal coordination : angle 0.95710 / 0.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 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 437 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 391 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 337 ILE cc_start: 0.9014 (mm) cc_final: 0.8804 (mt) REVERT: A 541 TYR cc_start: 0.8126 (m-10) cc_final: 0.7776 (m-10) REVERT: B 66 MET cc_start: 0.8875 (mmm) cc_final: 0.8568 (mmm) REVERT: B 541 TYR cc_start: 0.8113 (m-10) cc_final: 0.7775 (m-10) REVERT: C 66 MET cc_start: 0.8928 (mmm) cc_final: 0.8660 (mmm) REVERT: C 541 TYR cc_start: 0.8126 (m-10) cc_final: 0.7821 (m-10) REVERT: D 21 GLN cc_start: 0.6877 (mm110) cc_final: 0.6652 (mp10) REVERT: D 541 TYR cc_start: 0.8216 (m-10) cc_final: 0.7876 (m-10) outliers start: 46 outliers final: 30 residues processed: 423 average time/residue: 0.1477 time to fit residues: 100.6351 Evaluate side-chains 383 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 353 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 652 ASP 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 197 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 631 ILE 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 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 567 THR 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 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 25 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 255 optimal weight: 0.9980 chunk 213 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.159546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121091 restraints weight = 29487.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119677 restraints weight = 20144.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121913 restraints weight = 19469.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122148 restraints weight = 13839.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124073 restraints weight = 12775.508| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23024 Z= 0.153 Angle : 0.571 9.505 31116 Z= 0.289 Chirality : 0.040 0.199 3476 Planarity : 0.004 0.049 3828 Dihedral : 10.924 124.078 3272 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.67 % Allowed : 17.24 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.16), residues: 2644 helix: 2.11 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.36 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 165 TYR 0.019 0.001 TYR D 118 PHE 0.014 0.001 PHE C 341 TRP 0.011 0.001 TRP D 315 HIS 0.003 0.001 HIS D 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (23004) covalent geometry : angle 0.57096 / 0.29 (31096) SS BOND : bond 0.00174 / 0.09 ( 4) SS BOND : angle 0.21715 / 0.12 ( 8) hydrogen bonds : bond 0.03961 / 2.64 ( 1440) hydrogen bonds : angle 3.47910 / 2.47 ( 4248) metal coordination : bond 0.00186 / 0.15 ( 16) metal coordination : angle 0.98328 / 0.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 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 427 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 387 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8557 (mm) REVERT: A 742 ASN cc_start: 0.8148 (m-40) cc_final: 0.6706 (t0) REVERT: C 66 MET cc_start: 0.8876 (mmm) cc_final: 0.8626 (mmm) REVERT: C 442 MET cc_start: 0.8411 (mtp) cc_final: 0.8140 (mtm) REVERT: D 21 GLN cc_start: 0.7028 (mm110) cc_final: 0.6814 (mp10) REVERT: D 337 ILE cc_start: 0.9074 (mm) cc_final: 0.8870 (mt) REVERT: D 412 LEU cc_start: 0.9131 (mt) cc_final: 0.8928 (mt) REVERT: D 442 MET cc_start: 0.8408 (mtp) cc_final: 0.8140 (mtm) outliers start: 40 outliers final: 34 residues processed: 413 average time/residue: 0.1466 time to fit residues: 97.5398 Evaluate side-chains 384 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 349 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 ILE 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 114 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 153 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119621 restraints weight = 29472.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117956 restraints weight = 20062.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119618 restraints weight = 18953.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120773 restraints weight = 13356.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120964 restraints weight = 12178.246| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23024 Z= 0.181 Angle : 0.615 10.713 31116 Z= 0.309 Chirality : 0.042 0.248 3476 Planarity : 0.004 0.049 3828 Dihedral : 11.053 126.847 3272 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.75 % Allowed : 17.49 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.16), residues: 2644 helix: 2.06 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.32 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 512 TYR 0.037 0.002 TYR A 541 PHE 0.018 0.002 PHE A 540 TRP 0.012 0.001 TRP A 315 HIS 0.002 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (23004) covalent geometry : angle 0.61460 / 0.31 (31096) SS BOND : bond 0.00173 / 0.09 ( 4) SS BOND : angle 0.32019 / 0.18 ( 8) hydrogen bonds : bond 0.04181 / 2.77 ( 1440) hydrogen bonds : angle 3.59885 / 2.56 ( 4248) metal coordination : bond 0.00175 / 0.13 ( 16) metal coordination : angle 0.95920 / 0.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 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 421 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 379 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8901 (mm) cc_final: 0.8552 (mm) REVERT: A 628 TYR cc_start: 0.9007 (t80) cc_final: 0.8688 (t80) REVERT: A 742 ASN cc_start: 0.8255 (m-40) cc_final: 0.6795 (t0) REVERT: C 319 PHE cc_start: 0.7880 (m-80) cc_final: 0.7534 (m-80) REVERT: D 412 LEU cc_start: 0.9131 (mt) cc_final: 0.8924 (mt) REVERT: D 628 TYR cc_start: 0.8973 (t80) cc_final: 0.8671 (t80) outliers start: 42 outliers final: 36 residues processed: 405 average time/residue: 0.1473 time to fit residues: 96.1535 Evaluate side-chains 387 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 351 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 ILE 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 114 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 214 optimal weight: 0.0060 chunk 2 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120962 restraints weight = 29413.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119803 restraints weight = 19999.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121545 restraints weight = 18819.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122796 restraints weight = 12787.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123045 restraints weight = 11679.884| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23024 Z= 0.148 Angle : 0.602 10.644 31116 Z= 0.303 Chirality : 0.041 0.245 3476 Planarity : 0.004 0.050 3828 Dihedral : 10.992 125.141 3272 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.59 % Allowed : 18.16 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.16), residues: 2644 helix: 2.14 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -0.22 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 512 TYR 0.043 0.002 TYR B 541 PHE 0.015 0.001 PHE D 540 TRP 0.011 0.001 TRP B 315 HIS 0.002 0.001 HIS C 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (23004) covalent geometry : angle 0.60185 / 0.30 (31096) SS BOND : bond 0.00134 / 0.07 ( 4) SS BOND : angle 0.11562 / 0.07 ( 8) hydrogen bonds : bond 0.03995 / 2.65 ( 1440) hydrogen bonds : angle 3.54361 / 2.52 ( 4248) metal coordination : bond 0.00151 / 0.11 ( 16) metal coordination : angle 0.86998 / 0.50 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 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 411 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 373 time to evaluate : 0.782 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 90 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8552 (mm) REVERT: B 541 TYR cc_start: 0.8653 (m-10) cc_final: 0.8366 (m-80) REVERT: C 90 LEU cc_start: 0.8919 (mm) cc_final: 0.8555 (mm) REVERT: C 319 PHE cc_start: 0.7868 (m-80) cc_final: 0.7496 (m-80) REVERT: D 412 LEU cc_start: 0.9122 (mt) cc_final: 0.8916 (mt) outliers start: 38 outliers final: 33 residues processed: 397 average time/residue: 0.1419 time to fit residues: 91.5118 Evaluate side-chains 381 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 347 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 LEU 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 C residue 567 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 114 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 309 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3842 r_free = 0.3842 target = 0.158808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120810 restraints weight = 29326.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119217 restraints weight = 21001.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121003 restraints weight = 19216.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122551 restraints weight = 13038.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122736 restraints weight = 11744.026| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23024 Z= 0.153 Angle : 0.607 10.261 31116 Z= 0.309 Chirality : 0.041 0.260 3476 Planarity : 0.004 0.050 3828 Dihedral : 10.843 125.092 3272 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.59 % Allowed : 18.91 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.16), residues: 2644 helix: 2.13 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -0.18 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 512 TYR 0.039 0.002 TYR B 541 PHE 0.015 0.001 PHE D 540 TRP 0.012 0.001 TRP A 315 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (23004) covalent geometry : angle 0.60664 / 0.31 (31096) SS BOND : bond 0.00138 / 0.07 ( 4) SS BOND : angle 0.17766 / 0.10 ( 8) hydrogen bonds : bond 0.04014 / 2.66 ( 1440) hydrogen bonds : angle 3.55757 / 2.53 ( 4248) metal coordination : bond 0.00161 / 0.12 ( 16) metal coordination : angle 0.87707 / 0.51 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3318.44 seconds wall clock time: 58 minutes 29.92 seconds (3509.92 seconds total)