Starting phenix.real_space_refine on Sun Aug 24 22:15:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvw_34300/08_2025/8gvw_34300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvw_34300/08_2025/8gvw_34300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gvw_34300/08_2025/8gvw_34300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvw_34300/08_2025/8gvw_34300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gvw_34300/08_2025/8gvw_34300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvw_34300/08_2025/8gvw_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.62, per 1000 atoms: 0.25 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: 1.52 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.54 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: 3.16 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3577 1.32 - 1.44: 6127 1.44 - 1.57: 13088 1.57 - 1.69: 24 1.69 - 1.81: 188 Bond restraints: 23004 Sorted by residual: bond pdb=" O12 POV A 802 " pdb=" P POV A 802 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" O12 POV D 802 " pdb=" P POV D 802 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" CB PRO C 398 " pdb=" CG PRO C 398 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.56e+00 bond pdb=" O12 POV B 802 " pdb=" P POV B 802 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" O12 POV C 802 " pdb=" P POV C 802 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.55e+00 ... (remaining 22999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 29630 1.91 - 3.82: 1196 3.82 - 5.73: 199 5.73 - 7.65: 55 7.65 - 9.56: 16 Bond angle restraints: 31096 Sorted by residual: angle pdb=" CA PRO C 398 " pdb=" N PRO C 398 " pdb=" CD PRO C 398 " ideal model delta sigma weight residual 112.00 105.71 6.29 1.40e+00 5.10e-01 2.02e+01 angle pdb=" CA PRO A 398 " pdb=" N PRO A 398 " pdb=" CD PRO A 398 " ideal model delta sigma weight residual 112.00 105.74 6.26 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PRO B 398 " pdb=" N PRO B 398 " pdb=" CD PRO B 398 " ideal model delta sigma weight residual 112.00 105.74 6.26 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PRO D 398 " pdb=" N PRO D 398 " pdb=" CD PRO D 398 " ideal model delta sigma weight residual 112.00 105.78 6.22 1.40e+00 5.10e-01 1.97e+01 angle pdb=" CA PHE D 753 " pdb=" CB PHE D 753 " pdb=" CG PHE D 753 " ideal model delta sigma weight residual 113.80 117.54 -3.74 1.00e+00 1.00e+00 1.40e+01 ... (remaining 31091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 13720 34.94 - 69.87: 268 69.87 - 104.81: 28 104.81 - 139.74: 20 139.74 - 174.68: 4 Dihedral angle restraints: 14040 sinusoidal: 6096 harmonic: 7944 Sorted by residual: dihedral pdb=" C26 YZY C 806 " pdb=" C27 YZY C 806 " pdb=" C28 YZY C 806 " pdb=" C29 YZY C 806 " ideal model delta sinusoidal sigma weight residual 119.11 -55.57 174.68 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 807 " pdb=" C27 YZY A 807 " pdb=" C28 YZY A 807 " pdb=" C29 YZY A 807 " ideal model delta sinusoidal sigma weight residual 119.11 -55.56 174.67 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 806 " pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sinusoidal sigma weight residual 119.11 -55.53 174.64 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 14037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2724 0.052 - 0.105: 608 0.105 - 0.157: 120 0.157 - 0.209: 20 0.209 - 0.262: 4 Chirality restraints: 3476 Sorted by residual: chirality pdb=" CB VAL C 590 " pdb=" CA VAL C 590 " pdb=" CG1 VAL C 590 " pdb=" CG2 VAL C 590 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL D 590 " pdb=" CA VAL D 590 " pdb=" CG1 VAL D 590 " pdb=" CG2 VAL D 590 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL A 590 " pdb=" CA VAL A 590 " pdb=" CG1 VAL A 590 " pdb=" CG2 VAL A 590 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 3473 not shown) Planarity restraints: 3828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 397 " 0.049 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO B 398 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 398 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 398 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 397 " 0.049 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO A 398 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 398 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 398 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 397 " 0.049 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO C 398 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 398 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 398 " 0.039 5.00e-02 4.00e+02 ... (remaining 3825 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3938 2.77 - 3.30: 21644 3.30 - 3.83: 36931 3.83 - 4.37: 42327 4.37 - 4.90: 74193 Nonbonded interactions: 179033 Sorted by model distance: nonbonded pdb=" OH TYR C 374 " pdb=" O SER C 489 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 374 " pdb=" O SER A 489 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR D 374 " pdb=" O SER D 489 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR B 374 " pdb=" O SER B 489 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASP C 215 " pdb=" OH TYR C 713 " model vdw 2.288 3.040 ... (remaining 179028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 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: 0.000 Normalize map: mean=0, sd=1: 5.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.380 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 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 : 15.334 174.677 8860 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 aren 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 covalent geometry : bond 0.00564 (23004) covalent geometry : angle 0.89412 (31096) SS BOND : bond 0.00248 ( 4) SS BOND : angle 1.99070 ( 8) hydrogen bonds : bond 0.09118 ( 1440) hydrogen bonds : angle 4.45732 ( 4248) metal coordination : bond 0.00965 ( 16) metal coordination : angle 2.54639 ( 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 : 0.602 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8396 (pttm) cc_final: 0.7659 (pttm) REVERT: A 48 VAL cc_start: 0.9046 (t) cc_final: 0.8833 (p) REVERT: A 479 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 598 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8146 (mm-30) REVERT: A 628 TYR cc_start: 0.8945 (t80) cc_final: 0.8675 (t80) REVERT: A 728 MET cc_start: 0.7780 (ttp) cc_final: 0.7564 (ttp) REVERT: B 42 LYS cc_start: 0.8404 (pttm) cc_final: 0.7680 (pttm) REVERT: B 48 VAL cc_start: 0.9061 (t) cc_final: 0.8831 (p) REVERT: B 598 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8146 (mm-30) REVERT: B 628 TYR cc_start: 0.8936 (t80) cc_final: 0.8667 (t80) REVERT: C 42 LYS cc_start: 0.8408 (pttm) cc_final: 0.7639 (pttm) REVERT: C 48 VAL cc_start: 0.9086 (t) cc_final: 0.8873 (p) REVERT: C 598 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8112 (mm-30) REVERT: C 628 TYR cc_start: 0.8943 (t80) cc_final: 0.8627 (t80) REVERT: C 728 MET cc_start: 0.7835 (ttp) cc_final: 0.7612 (ttp) REVERT: D 42 LYS cc_start: 0.8408 (pttm) cc_final: 0.7649 (pttm) REVERT: D 541 TYR cc_start: 0.7959 (m-10) cc_final: 0.7759 (m-10) REVERT: D 728 MET cc_start: 0.7812 (ttp) cc_final: 0.7597 (ttp) outliers start: 4 outliers final: 0 residues processed: 515 average time/residue: 0.1151 time to fit residues: 97.4169 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 : 0.714 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3925 r_free = 0.3925 target = 0.165783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125992 restraints weight = 29282.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128069 restraints weight = 18279.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129236 restraints weight = 12634.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129426 restraints weight = 10595.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129510 restraints weight = 9964.394| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1424 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= 0.125 Angle : 0.548 6.687 31116 Z= 0.283 Chirality : 0.039 0.158 3476 Planarity : 0.004 0.046 3828 Dihedral : 12.483 119.060 3576 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.50 % Allowed : 10.56 % Favored : 88.94 % 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 aren not related in a simple way. whole: 1.30 (0.16), residues: 2644 helix: 1.37 (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 C 263 TYR 0.015 0.001 TYR C 118 PHE 0.013 0.001 PHE C 540 TRP 0.011 0.001 TRP A 315 HIS 0.003 0.001 HIS D 712 Details of bonding type rmsd covalent geometry : bond 0.00288 (23004) covalent geometry : angle 0.54751 (31096) SS BOND : bond 0.00189 ( 4) SS BOND : angle 0.34327 ( 8) hydrogen bonds : bond 0.04058 ( 1440) hydrogen bonds : angle 3.62994 ( 4248) metal coordination : bond 0.00336 ( 16) metal coordination : angle 1.75426 ( 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 423 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 411 time to evaluate : 0.760 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: 0.8930 (mm) cc_final: 0.8560 (mm) REVERT: A 337 ILE cc_start: 0.8957 (mm) cc_final: 0.8711 (mt) REVERT: A 479 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 541 TYR cc_start: 0.7859 (m-10) cc_final: 0.7506 (m-10) REVERT: B 65 CYS cc_start: 0.8276 (p) cc_final: 0.7968 (p) REVERT: B 114 LEU cc_start: 0.8935 (mm) cc_final: 0.8571 (mm) REVERT: B 337 ILE cc_start: 0.8968 (mm) cc_final: 0.8724 (mt) REVERT: B 541 TYR cc_start: 0.7874 (m-10) cc_final: 0.7571 (m-10) REVERT: C 65 CYS cc_start: 0.8282 (p) cc_final: 0.7961 (p) REVERT: C 114 LEU cc_start: 0.8949 (mm) cc_final: 0.8592 (mm) REVERT: C 337 ILE cc_start: 0.8955 (mm) cc_final: 0.8703 (mt) REVERT: C 340 LEU cc_start: 0.9269 (mt) cc_final: 0.9061 (mp) REVERT: C 541 TYR cc_start: 0.7863 (m-10) cc_final: 0.7553 (m-10) REVERT: D 114 LEU cc_start: 0.8960 (mm) cc_final: 0.8603 (mm) REVERT: D 337 ILE cc_start: 0.8933 (mm) cc_final: 0.8677 (mt) REVERT: D 340 LEU cc_start: 0.9234 (mt) cc_final: 0.9019 (mp) REVERT: D 427 PHE cc_start: 0.7910 (t80) cc_final: 0.7596 (t80) REVERT: D 541 TYR cc_start: 0.8068 (m-10) cc_final: 0.7670 (m-10) outliers start: 12 outliers final: 8 residues processed: 417 average time/residue: 0.1137 time to fit residues: 78.6289 Evaluate side-chains 362 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 354 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 383 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 50 optimal weight: 2.9990 chunk 260 optimal weight: 0.7980 chunk 256 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 100 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.164263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122844 restraints weight = 28911.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125257 restraints weight = 14831.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128621 restraints weight = 10501.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128568 restraints weight = 8947.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128651 restraints weight = 8494.379| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1785 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= 0.120 Angle : 0.516 8.508 31116 Z= 0.265 Chirality : 0.038 0.157 3476 Planarity : 0.004 0.046 3828 Dihedral : 11.285 113.658 3576 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.83 % Allowed : 12.94 % Favored : 86.23 % 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 aren not related in a simple way. whole: 1.79 (0.16), residues: 2644 helix: 1.76 (0.12), residues: 1972 sheet: None (None), residues: 0 loop : -0.45 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 191 TYR 0.018 0.001 TYR D 118 PHE 0.012 0.001 PHE D 540 TRP 0.011 0.001 TRP C 410 HIS 0.003 0.001 HIS B 735 Details of bonding type rmsd covalent geometry : bond 0.00269 (23004) covalent geometry : angle 0.51582 (31096) SS BOND : bond 0.00125 ( 4) SS BOND : angle 0.19647 ( 8) hydrogen bonds : bond 0.03849 ( 1440) hydrogen bonds : angle 3.46195 ( 4248) metal coordination : bond 0.00233 ( 16) metal coordination : angle 1.48265 ( 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 404 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 384 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 65 CYS cc_start: 0.8208 (p) cc_final: 0.7732 (p) REVERT: A 114 LEU cc_start: 0.8993 (mm) cc_final: 0.8668 (mm) REVERT: A 479 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7262 (mm-30) REVERT: A 539 TYR cc_start: 0.9186 (m-80) cc_final: 0.8831 (m-80) REVERT: A 541 TYR cc_start: 0.8006 (m-10) cc_final: 0.7543 (m-10) REVERT: B 114 LEU cc_start: 0.8998 (mm) cc_final: 0.8671 (mm) REVERT: B 337 ILE cc_start: 0.8868 (mm) cc_final: 0.8598 (mt) REVERT: B 539 TYR cc_start: 0.9185 (m-80) cc_final: 0.8847 (m-80) REVERT: B 541 TYR cc_start: 0.7996 (m-10) cc_final: 0.7531 (m-10) REVERT: C 114 LEU cc_start: 0.8970 (mm) cc_final: 0.8659 (mm) REVERT: C 337 ILE cc_start: 0.8888 (mm) cc_final: 0.8630 (mt) REVERT: C 479 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7145 (mm-30) REVERT: C 539 TYR cc_start: 0.9181 (m-80) cc_final: 0.8839 (m-80) REVERT: C 541 TYR cc_start: 0.8001 (m-10) cc_final: 0.7537 (m-10) REVERT: C 744 LYS cc_start: 0.7007 (mttt) cc_final: 0.6674 (mttp) REVERT: D 65 CYS cc_start: 0.8236 (p) cc_final: 0.7758 (p) REVERT: D 114 LEU cc_start: 0.8971 (mm) cc_final: 0.8661 (mm) REVERT: D 337 ILE cc_start: 0.8871 (mm) cc_final: 0.8609 (mt) REVERT: D 479 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7163 (mm-30) REVERT: D 539 TYR cc_start: 0.9188 (m-80) cc_final: 0.8841 (m-80) REVERT: D 541 TYR cc_start: 0.8115 (m-10) cc_final: 0.7798 (m-10) outliers start: 20 outliers final: 19 residues processed: 396 average time/residue: 0.1144 time to fit residues: 74.6506 Evaluate side-chains 361 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 342 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 134 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122923 restraints weight = 29469.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.121806 restraints weight = 19925.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123239 restraints weight = 20811.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124471 restraints weight = 14128.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125098 restraints weight = 12776.895| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2190 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= 0.156 Angle : 0.547 9.986 31116 Z= 0.276 Chirality : 0.040 0.210 3476 Planarity : 0.004 0.047 3828 Dihedral : 11.047 120.527 3576 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.67 % Allowed : 13.36 % Favored : 84.97 % 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 aren not related in a simple way. whole: 1.97 (0.16), residues: 2644 helix: 1.90 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.43 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 512 TYR 0.015 0.001 TYR D 524 PHE 0.013 0.002 PHE B 341 TRP 0.013 0.001 TRP C 315 HIS 0.003 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00371 (23004) covalent geometry : angle 0.54656 (31096) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.29899 ( 8) hydrogen bonds : bond 0.03999 ( 1440) hydrogen bonds : angle 3.46074 ( 4248) metal coordination : bond 0.00242 ( 16) metal coordination : angle 1.28197 ( 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 420 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 380 time to evaluate : 0.788 Fit side-chains REVERT: A 479 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 539 TYR cc_start: 0.9190 (m-80) cc_final: 0.8862 (m-80) REVERT: A 541 TYR cc_start: 0.8141 (m-10) cc_final: 0.7836 (m-10) REVERT: B 539 TYR cc_start: 0.9193 (m-80) cc_final: 0.8886 (m-80) REVERT: B 541 TYR cc_start: 0.8102 (m-10) cc_final: 0.7697 (m-10) REVERT: C 147 MET cc_start: 0.8010 (mtp) cc_final: 0.7738 (mtp) REVERT: C 157 ILE cc_start: 0.8392 (mm) cc_final: 0.8136 (mm) REVERT: C 539 TYR cc_start: 0.9188 (m-80) cc_final: 0.8876 (m-80) REVERT: C 541 TYR cc_start: 0.8112 (m-10) cc_final: 0.7703 (m-10) REVERT: D 539 TYR cc_start: 0.9182 (m-80) cc_final: 0.8866 (m-80) REVERT: D 541 TYR cc_start: 0.8172 (m-10) cc_final: 0.7750 (m-10) outliers start: 40 outliers final: 30 residues processed: 406 average time/residue: 0.1241 time to fit residues: 82.2902 Evaluate side-chains 381 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 351 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 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 115 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 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 115 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 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: 0.3980 chunk 117 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 257 optimal weight: 0.6980 chunk 240 optimal weight: 3.9990 chunk 245 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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** D 711 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.162278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123231 restraints weight = 29184.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121857 restraints weight = 18779.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123575 restraints weight = 17900.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124553 restraints weight = 12860.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124783 restraints weight = 12024.982| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23024 Z= 0.123 Angle : 0.528 9.255 31116 Z= 0.262 Chirality : 0.038 0.209 3476 Planarity : 0.004 0.048 3828 Dihedral : 10.953 119.821 3576 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.46 % Allowed : 14.15 % Favored : 84.39 % 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 aren not related in a simple way. whole: 2.11 (0.16), residues: 2644 helix: 2.02 (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 D 754 TYR 0.015 0.001 TYR B 524 PHE 0.013 0.001 PHE C 341 TRP 0.010 0.001 TRP C 315 HIS 0.003 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00284 (23004) covalent geometry : angle 0.52735 (31096) SS BOND : bond 0.00125 ( 4) SS BOND : angle 0.12339 ( 8) hydrogen bonds : bond 0.03771 ( 1440) hydrogen bonds : angle 3.40018 ( 4248) metal coordination : bond 0.00197 ( 16) metal coordination : angle 1.07184 ( 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 417 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 382 time to evaluate : 0.737 Fit side-chains REVERT: A 66 MET cc_start: 0.8886 (mmm) cc_final: 0.8635 (mmm) REVERT: A 539 TYR cc_start: 0.9141 (m-80) cc_final: 0.8918 (m-80) REVERT: A 744 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7133 (mttp) REVERT: B 66 MET cc_start: 0.8870 (mmm) cc_final: 0.8625 (mmm) REVERT: B 539 TYR cc_start: 0.9150 (m-80) cc_final: 0.8921 (m-80) REVERT: C 147 MET cc_start: 0.7995 (mtp) cc_final: 0.7702 (mtp) REVERT: C 539 TYR cc_start: 0.9143 (m-80) cc_final: 0.8912 (m-80) REVERT: D 21 GLN cc_start: 0.6668 (mm110) cc_final: 0.6428 (mp10) REVERT: D 66 MET cc_start: 0.8894 (mmm) cc_final: 0.8635 (mmm) REVERT: D 147 MET cc_start: 0.7989 (mtp) cc_final: 0.7717 (mtp) REVERT: D 157 ILE cc_start: 0.8446 (mm) cc_final: 0.8169 (mm) REVERT: D 539 TYR cc_start: 0.9138 (m-80) cc_final: 0.8925 (m-80) outliers start: 35 outliers final: 29 residues processed: 411 average time/residue: 0.1152 time to fit residues: 77.4539 Evaluate side-chains 387 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 357 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 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 744 LYS 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 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 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 525 CYS Chi-restraints excluded: chain D residue 567 THR 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: 0.7980 chunk 27 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 249 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3861 r_free = 0.3861 target = 0.160510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121368 restraints weight = 29699.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119915 restraints weight = 19691.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121750 restraints weight = 18313.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122547 restraints weight = 13143.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122798 restraints weight = 12230.993| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23024 Z= 0.145 Angle : 0.541 8.943 31116 Z= 0.270 Chirality : 0.039 0.201 3476 Planarity : 0.004 0.048 3828 Dihedral : 10.983 122.721 3576 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.88 % Allowed : 15.48 % Favored : 82.64 % 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 aren not related in a simple way. whole: 2.17 (0.16), residues: 2644 helix: 2.07 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.41 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 754 TYR 0.016 0.001 TYR B 524 PHE 0.015 0.001 PHE A 540 TRP 0.012 0.001 TRP C 315 HIS 0.003 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00344 (23004) covalent geometry : angle 0.54074 (31096) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.26269 ( 8) hydrogen bonds : bond 0.03899 ( 1440) hydrogen bonds : angle 3.42529 ( 4248) metal coordination : bond 0.00219 ( 16) metal coordination : angle 1.05533 ( 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 435 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 390 time to evaluate : 0.700 Fit side-chains REVERT: A 66 MET cc_start: 0.8816 (mmm) cc_final: 0.8538 (mmm) REVERT: A 471 MET cc_start: 0.8552 (tmm) cc_final: 0.8341 (tmm) REVERT: A 541 TYR cc_start: 0.8161 (m-10) cc_final: 0.7767 (m-10) REVERT: B 75 LEU cc_start: 0.8865 (mt) cc_final: 0.8554 (mm) REVERT: B 471 MET cc_start: 0.8545 (tmm) cc_final: 0.8335 (tmm) REVERT: B 539 TYR cc_start: 0.9149 (m-80) cc_final: 0.8942 (m-80) REVERT: B 541 TYR cc_start: 0.8261 (m-80) cc_final: 0.7782 (m-10) REVERT: C 442 MET cc_start: 0.8375 (mtp) cc_final: 0.8092 (mtm) REVERT: C 471 MET cc_start: 0.8542 (tmm) cc_final: 0.8326 (tmm) REVERT: C 539 TYR cc_start: 0.9143 (m-80) cc_final: 0.8933 (m-80) REVERT: C 541 TYR cc_start: 0.8236 (m-80) cc_final: 0.7783 (m-10) REVERT: D 21 GLN cc_start: 0.6781 (mm110) cc_final: 0.6558 (mp10) REVERT: D 442 MET cc_start: 0.8372 (mtp) cc_final: 0.8090 (mtm) REVERT: D 471 MET cc_start: 0.8546 (tmm) cc_final: 0.8332 (tmm) REVERT: D 541 TYR cc_start: 0.8180 (m-10) cc_final: 0.7795 (m-10) outliers start: 45 outliers final: 27 residues processed: 424 average time/residue: 0.1214 time to fit residues: 83.6385 Evaluate side-chains 395 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 368 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 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 343 MET 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 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: 2.9990 chunk 84 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN 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 = 0.158962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119910 restraints weight = 29547.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119201 restraints weight = 18848.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120667 restraints weight = 17370.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121318 restraints weight = 12794.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121600 restraints weight = 11919.691| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23024 Z= 0.167 Angle : 0.558 7.747 31116 Z= 0.282 Chirality : 0.040 0.183 3476 Planarity : 0.004 0.049 3828 Dihedral : 11.122 125.360 3576 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.54 % Allowed : 16.65 % Favored : 81.80 % 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 aren not related in a simple way. whole: 2.17 (0.16), residues: 2644 helix: 2.04 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.33 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 165 TYR 0.019 0.001 TYR A 118 PHE 0.014 0.002 PHE B 341 TRP 0.012 0.001 TRP C 315 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00398 (23004) covalent geometry : angle 0.55825 (31096) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.29993 ( 8) hydrogen bonds : bond 0.04061 ( 1440) hydrogen bonds : angle 3.48499 ( 4248) metal coordination : bond 0.00211 ( 16) metal coordination : angle 1.03888 ( 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 438 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 401 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.6964 (mm110) cc_final: 0.6705 (mp10) REVERT: A 471 MET cc_start: 0.8558 (tmm) cc_final: 0.8338 (tmm) REVERT: A 479 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7295 (mm-30) REVERT: A 541 TYR cc_start: 0.8120 (m-10) cc_final: 0.7834 (m-10) REVERT: B 471 MET cc_start: 0.8556 (tmm) cc_final: 0.8341 (tmm) REVERT: B 541 TYR cc_start: 0.8250 (m-80) cc_final: 0.7960 (m-10) REVERT: C 471 MET cc_start: 0.8550 (tmm) cc_final: 0.8333 (tmm) REVERT: C 541 TYR cc_start: 0.8257 (m-80) cc_final: 0.7959 (m-10) REVERT: D 471 MET cc_start: 0.8550 (tmm) cc_final: 0.8336 (tmm) REVERT: D 541 TYR cc_start: 0.8283 (m-10) cc_final: 0.7781 (m-10) outliers start: 37 outliers final: 27 residues processed: 424 average time/residue: 0.1122 time to fit residues: 76.4331 Evaluate side-chains 381 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 354 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 341 PHE 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 114 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 38 ASN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 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 725 VAL Chi-restraints excluded: chain D residue 108 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 25 optimal weight: 0.7980 chunk 152 optimal weight: 0.1980 chunk 125 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 235 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** 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 = 0.3867 r_free = 0.3867 target = 0.161239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122751 restraints weight = 29167.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.121789 restraints weight = 19209.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123130 restraints weight = 20157.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124596 restraints weight = 13632.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125063 restraints weight = 12188.313| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23024 Z= 0.123 Angle : 0.548 9.629 31116 Z= 0.277 Chirality : 0.039 0.191 3476 Planarity : 0.004 0.050 3828 Dihedral : 10.996 121.957 3576 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.21 % Allowed : 17.61 % Favored : 81.18 % 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 aren not related in a simple way. whole: 2.29 (0.16), residues: 2644 helix: 2.13 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -0.29 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 754 TYR 0.019 0.001 TYR D 118 PHE 0.014 0.001 PHE C 36 TRP 0.010 0.001 TRP C 315 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00286 (23004) covalent geometry : angle 0.54766 (31096) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.04162 ( 8) hydrogen bonds : bond 0.03805 ( 1440) hydrogen bonds : angle 3.45420 ( 4248) metal coordination : bond 0.00186 ( 16) metal coordination : angle 0.85286 ( 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 418 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 389 time to evaluate : 0.770 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: 0.8881 (OUTLIER) cc_final: 0.8466 (mm) REVERT: A 443 ASN cc_start: 0.8754 (m110) cc_final: 0.8552 (m110) REVERT: B 90 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8451 (mm) REVERT: B 443 ASN cc_start: 0.8727 (m110) cc_final: 0.8526 (m110) outliers start: 29 outliers final: 24 residues processed: 405 average time/residue: 0.1258 time to fit residues: 82.2360 Evaluate side-chains 378 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 352 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 B residue 32 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 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 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 631 ILE 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 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: 0.6980 chunk 141 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 211 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** 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 = 0.3858 r_free = 0.3858 target = 0.160103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121596 restraints weight = 29357.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120101 restraints weight = 19031.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121911 restraints weight = 18755.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122944 restraints weight = 13135.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123259 restraints weight = 12075.966| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23024 Z= 0.140 Angle : 0.577 9.519 31116 Z= 0.291 Chirality : 0.040 0.234 3476 Planarity : 0.004 0.056 3828 Dihedral : 11.008 122.440 3576 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.42 % Allowed : 17.99 % Favored : 80.59 % 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 aren not related in a simple way. whole: 2.28 (0.17), residues: 2644 helix: 2.12 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.30 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 165 TYR 0.020 0.001 TYR D 118 PHE 0.014 0.001 PHE C 36 TRP 0.011 0.001 TRP D 315 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00330 (23004) covalent geometry : angle 0.57664 (31096) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.17168 ( 8) hydrogen bonds : bond 0.03879 ( 1440) hydrogen bonds : angle 3.48463 ( 4248) metal coordination : bond 0.00209 ( 16) metal coordination : angle 0.87219 ( 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 408 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 374 time to evaluate : 0.663 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: 0.8867 (mm) cc_final: 0.8502 (mm) REVERT: A 628 TYR cc_start: 0.8930 (t80) cc_final: 0.8647 (t80) REVERT: B 90 LEU cc_start: 0.8908 (mm) cc_final: 0.8540 (mm) REVERT: C 90 LEU cc_start: 0.8890 (mm) cc_final: 0.8496 (mm) outliers start: 34 outliers final: 26 residues processed: 391 average time/residue: 0.1186 time to fit residues: 75.3246 Evaluate side-chains 371 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 345 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 343 MET 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 32 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 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 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 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 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: 0.0770 chunk 2 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 250 optimal weight: 0.0570 chunk 207 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 chunk 89 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123414 restraints weight = 29361.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121917 restraints weight = 19927.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124157 restraints weight = 19051.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124571 restraints weight = 13310.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125725 restraints weight = 12327.138| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3296 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= 0.121 Angle : 0.573 9.499 31116 Z= 0.290 Chirality : 0.040 0.215 3476 Planarity : 0.004 0.051 3828 Dihedral : 10.885 120.450 3576 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.04 % Allowed : 19.03 % Favored : 79.92 % 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 aren not related in a simple way. whole: 2.32 (0.17), residues: 2644 helix: 2.16 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -0.28 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 165 TYR 0.022 0.001 TYR B 446 PHE 0.014 0.001 PHE C 540 TRP 0.010 0.001 TRP D 315 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00278 (23004) covalent geometry : angle 0.57305 (31096) SS BOND : bond 0.00109 ( 4) SS BOND : angle 0.03381 ( 8) hydrogen bonds : bond 0.03739 ( 1440) hydrogen bonds : angle 3.47630 ( 4248) metal coordination : bond 0.00187 ( 16) metal coordination : angle 0.81239 ( 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 397 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 372 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 90 LEU cc_start: 0.8868 (mm) cc_final: 0.8502 (mm) REVERT: A 380 MET cc_start: 0.7801 (mtm) cc_final: 0.7561 (mtm) REVERT: A 479 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7146 (mm-30) REVERT: A 541 TYR cc_start: 0.8095 (m-10) cc_final: 0.7819 (m-10) REVERT: A 595 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7400 (tt0) REVERT: B 90 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8566 (mm) REVERT: B 595 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7427 (tt0) REVERT: C 67 ASP cc_start: 0.7603 (p0) cc_final: 0.7375 (p0) REVERT: C 90 LEU cc_start: 0.8843 (mm) cc_final: 0.8476 (mm) REVERT: C 595 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7416 (tt0) outliers start: 25 outliers final: 22 residues processed: 383 average time/residue: 0.1199 time to fit residues: 74.0392 Evaluate side-chains 364 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 341 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 343 MET Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain C residue 108 VAL 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 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 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 114 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 188 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 309 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 = 0.3845 r_free = 0.3845 target = 0.158831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120211 restraints weight = 29473.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121407 restraints weight = 18332.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122367 restraints weight = 15422.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122845 restraints weight = 11299.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123147 restraints weight = 10692.421| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23024 Z= 0.159 Angle : 0.615 10.254 31116 Z= 0.310 Chirality : 0.041 0.234 3476 Planarity : 0.004 0.050 3828 Dihedral : 10.913 123.630 3576 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.42 % Allowed : 19.57 % Favored : 79.01 % 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 aren not related in a simple way. whole: 2.30 (0.17), residues: 2644 helix: 2.11 (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 0.004 0.000 ARG C 165 TYR 0.020 0.001 TYR D 118 PHE 0.014 0.001 PHE B 341 TRP 0.012 0.001 TRP D 315 HIS 0.003 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00383 (23004) covalent geometry : angle 0.61495 (31096) SS BOND : bond 0.00145 ( 4) SS BOND : angle 0.26827 ( 8) hydrogen bonds : bond 0.03975 ( 1440) hydrogen bonds : angle 3.54546 ( 4248) metal coordination : bond 0.00197 ( 16) metal coordination : angle 0.87096 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.66 seconds wall clock time: 49 minutes 51.17 seconds (2991.17 seconds total)