Starting phenix.real_space_refine on Fri Feb 6 04:00:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khj_62344/02_2026/9khj_62344.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khj_62344/02_2026/9khj_62344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9khj_62344/02_2026/9khj_62344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khj_62344/02_2026/9khj_62344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9khj_62344/02_2026/9khj_62344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khj_62344/02_2026/9khj_62344.map" } resolution = 2.62 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= 0.017 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 14588 2.51 5 N 3600 2.21 5 O 3940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22260 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5408 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5408 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5408 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5408 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "A" 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: "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: "D" 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS A 176 34.461 33.506 74.129 1.00115.46 S ATOM 1162 SG CYS A 178 31.483 33.707 76.650 1.00120.75 S ATOM 1184 SG CYS A 181 33.624 36.591 76.698 1.00112.87 S ATOM 6556 SG CYS C 176 97.833 98.778 74.135 1.00115.46 S ATOM 6570 SG CYS C 178 100.811 98.578 76.656 1.00120.75 S ATOM 6592 SG CYS C 181 98.671 95.694 76.705 1.00112.87 S ATOM 11964 SG CYS B 176 98.788 34.446 74.126 1.00115.46 S ATOM 11978 SG CYS B 178 98.589 31.467 76.646 1.00120.75 S ATOM 12000 SG CYS B 181 95.704 33.607 76.696 1.00112.87 S ATOM 17372 SG CYS D 176 33.497 97.842 74.126 1.00115.46 S ATOM 17386 SG CYS D 178 33.696 100.821 76.646 1.00120.75 S ATOM 17408 SG CYS D 181 36.581 98.681 76.695 1.00112.87 S Time building chain proxies: 5.11, per 1000 atoms: 0.23 Number of scatterers: 22260 At special positions: 0 Unit cell: (133.136, 133.136, 137.376, 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 3940 8.00 N 3600 7.00 C 14588 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 C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 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: 1.98 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 181 " 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 178 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 181 " 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 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 181 " 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 178 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 176 " Number of angles added : 12 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5200 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 4 sheets defined 76.0% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 4.034A pdb=" N MET A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 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 213 Processing helix chain 'A' and resid 215 through 232 removed outlier: 4.048A pdb=" N LYS A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 257 removed outlier: 3.725A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 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 321 through 325 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 362 through 385 removed outlier: 4.062A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 424 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 426 through 431 removed outlier: 4.003A pdb=" N ILE A 431 " --> pdb=" O PHE A 427 " (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: 3.517A pdb=" N LEU A 496 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 499 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 4.527A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.353A 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 549 through 553 Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.672A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 588 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 removed outlier: 3.693A pdb=" N VAL A 615 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 632 removed outlier: 3.501A pdb=" N LEU A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 649 removed outlier: 3.639A pdb=" N SER A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 732 Processing helix chain 'A' and resid 734 through 758 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 4.034A pdb=" N MET C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 107 Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 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 213 Processing helix chain 'C' and resid 215 through 232 removed outlier: 4.048A pdb=" N LYS C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 257 removed outlier: 3.725A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 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 321 through 325 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 362 through 385 removed outlier: 4.063A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 424 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 426 through 431 removed outlier: 4.003A pdb=" N ILE C 431 " --> pdb=" O PHE C 427 " (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: 3.517A pdb=" N LEU C 496 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 499 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 4.527A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.353A 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 549 through 553 Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.672A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 588 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 removed outlier: 3.693A pdb=" N VAL C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 632 removed outlier: 3.501A pdb=" N LEU C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 649 removed outlier: 3.639A pdb=" N SER C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 732 Processing helix chain 'C' and resid 734 through 758 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 4.035A pdb=" N MET B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 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 213 Processing helix chain 'B' and resid 215 through 232 removed outlier: 4.048A pdb=" N LYS B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 257 removed outlier: 3.725A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 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 321 through 325 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 362 through 385 removed outlier: 4.062A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 424 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 426 through 431 removed outlier: 4.003A pdb=" N ILE B 431 " --> pdb=" O PHE B 427 " (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: 3.517A pdb=" N LEU B 496 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 499 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 4.527A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.353A 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 549 through 553 Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.672A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 588 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 removed outlier: 3.694A pdb=" N VAL B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 632 removed outlier: 3.501A pdb=" N LEU B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 649 removed outlier: 3.639A pdb=" N SER B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 732 Processing helix chain 'B' and resid 734 through 758 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 46 through 58 Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 4.035A pdb=" N MET D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 107 Processing helix chain 'D' and resid 108 through 117 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 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 213 Processing helix chain 'D' and resid 215 through 232 removed outlier: 4.047A pdb=" N LYS D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 257 removed outlier: 3.725A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 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 321 through 325 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 362 through 385 removed outlier: 4.063A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 424 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 426 through 431 removed outlier: 4.003A pdb=" N ILE D 431 " --> pdb=" O PHE D 427 " (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: 3.516A pdb=" N LEU D 496 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 499 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 4.527A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.352A 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 549 through 553 Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.672A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR D 588 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 615 removed outlier: 3.693A pdb=" N VAL D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 632 removed outlier: 3.500A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 649 removed outlier: 3.640A pdb=" N SER D 649 " --> pdb=" O LYS D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 732 Processing helix chain 'D' and resid 734 through 758 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 removed outlier: 4.395A pdb=" N ILE A 18 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE D 168 " --> pdb=" O ILE A 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 4.351A pdb=" N ILE A 168 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 18 " --> pdb=" O ILE A 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 18 through 19 removed outlier: 4.417A pdb=" N ILE C 18 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE B 168 " --> pdb=" O ILE C 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 167 through 168 removed outlier: 4.361A pdb=" N ILE C 168 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE D 18 " --> pdb=" O ILE C 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 1404 hydrogen bonds defined for protein. 4104 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: 3.58 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3504 1.31 - 1.43: 6065 1.43 - 1.56: 12991 1.56 - 1.69: 16 1.69 - 1.81: 188 Bond restraints: 22764 Sorted by residual: bond pdb=" C3 YZY B 806 " pdb=" O2 YZY B 806 " ideal model delta sigma weight residual 1.332 1.407 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C3 YZY D 806 " pdb=" O2 YZY D 806 " ideal model delta sigma weight residual 1.332 1.407 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C3 YZY C 806 " pdb=" O2 YZY C 806 " ideal model delta sigma weight residual 1.332 1.407 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C3 YZY A 806 " pdb=" O2 YZY A 806 " ideal model delta sigma weight residual 1.332 1.407 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C20 YZY A 806 " pdb=" O4 YZY A 806 " ideal model delta sigma weight residual 1.328 1.397 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 22759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 30001 2.11 - 4.23: 687 4.23 - 6.34: 92 6.34 - 8.45: 24 8.45 - 10.56: 16 Bond angle restraints: 30820 Sorted by residual: angle pdb=" CA MET A 343 " pdb=" C MET A 343 " pdb=" O MET A 343 " ideal model delta sigma weight residual 121.94 116.72 5.22 1.15e+00 7.56e-01 2.06e+01 angle pdb=" CA MET C 343 " pdb=" C MET C 343 " pdb=" O MET C 343 " ideal model delta sigma weight residual 121.94 116.72 5.22 1.15e+00 7.56e-01 2.06e+01 angle pdb=" CA MET D 343 " pdb=" C MET D 343 " pdb=" O MET D 343 " ideal model delta sigma weight residual 121.94 116.75 5.19 1.15e+00 7.56e-01 2.04e+01 angle pdb=" CA MET B 343 " pdb=" C MET B 343 " pdb=" O MET B 343 " ideal model delta sigma weight residual 121.94 116.75 5.19 1.15e+00 7.56e-01 2.04e+01 angle pdb=" N PRO D 342 " pdb=" CA PRO D 342 " pdb=" C PRO D 342 " ideal model delta sigma weight residual 113.53 108.00 5.53 1.39e+00 5.18e-01 1.58e+01 ... (remaining 30815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.74: 13179 32.74 - 65.47: 641 65.47 - 98.21: 48 98.21 - 130.94: 12 130.94 - 163.68: 4 Dihedral angle restraints: 13884 sinusoidal: 5892 harmonic: 7992 Sorted by residual: dihedral pdb=" C5 YZY D 806 " pdb=" C3 YZY D 806 " pdb=" C4 YZY D 806 " pdb=" O2 YZY D 806 " ideal model delta sinusoidal sigma weight residual 177.74 -18.58 -163.68 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C5 YZY B 806 " pdb=" C3 YZY B 806 " pdb=" C4 YZY B 806 " pdb=" O2 YZY B 806 " ideal model delta sinusoidal sigma weight residual 177.74 -18.58 -163.68 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C5 YZY A 806 " pdb=" C3 YZY A 806 " pdb=" C4 YZY A 806 " pdb=" O2 YZY A 806 " ideal model delta sinusoidal sigma weight residual 177.74 -18.62 -163.64 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 13881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2968 0.057 - 0.113: 434 0.113 - 0.170: 46 0.170 - 0.227: 12 0.227 - 0.284: 8 Chirality restraints: 3468 Sorted by residual: chirality pdb=" CA MET C 343 " pdb=" N MET C 343 " pdb=" C MET C 343 " pdb=" CB MET C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA MET A 343 " pdb=" N MET A 343 " pdb=" C MET A 343 " pdb=" CB MET A 343 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA MET B 343 " pdb=" N MET B 343 " pdb=" C MET B 343 " pdb=" CB MET B 343 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3465 not shown) Planarity restraints: 3808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 802 " -0.036 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C29 POV B 802 " 0.086 2.00e-02 2.50e+03 pdb="C210 POV B 802 " -0.086 2.00e-02 2.50e+03 pdb="C211 POV B 802 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 802 " 0.036 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C29 POV A 802 " -0.086 2.00e-02 2.50e+03 pdb="C210 POV A 802 " 0.086 2.00e-02 2.50e+03 pdb="C211 POV A 802 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 802 " -0.036 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C29 POV C 802 " 0.085 2.00e-02 2.50e+03 pdb="C210 POV C 802 " -0.086 2.00e-02 2.50e+03 pdb="C211 POV C 802 " 0.036 2.00e-02 2.50e+03 ... (remaining 3805 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 364 2.71 - 3.26: 21018 3.26 - 3.80: 34477 3.80 - 4.35: 43192 4.35 - 4.90: 74729 Nonbonded interactions: 173780 Sorted by model distance: nonbonded pdb=" O ILE D 209 " pdb=" OG SER D 213 " model vdw 2.160 3.040 nonbonded pdb=" O ILE C 209 " pdb=" OG SER C 213 " model vdw 2.160 3.040 nonbonded pdb=" O ILE B 209 " pdb=" OG SER B 213 " model vdw 2.160 3.040 nonbonded pdb=" O ILE A 209 " pdb=" OG SER A 213 " model vdw 2.160 3.040 nonbonded pdb=" O ASN C 551 " pdb=" ND2 ASN C 551 " model vdw 2.161 3.120 ... (remaining 173775 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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 individual isotropic 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.690 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.005 0.075 22784 Z= 0.293 Angle : 0.749 11.856 30840 Z= 0.413 Chirality : 0.043 0.284 3468 Planarity : 0.005 0.066 3808 Dihedral : 18.207 163.678 8672 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.35 % Allowed : 20.19 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.16), residues: 2668 helix: 2.29 (0.12), residues: 1932 sheet: None (None), residues: 0 loop : -1.33 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 71 TYR 0.014 0.001 TYR B 524 PHE 0.014 0.001 PHE D 301 TRP 0.012 0.001 TRP D 315 HIS 0.001 0.000 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00477 (22764) covalent geometry : angle 0.72756 (30820) SS BOND : bond 0.00180 ( 4) SS BOND : angle 0.39162 ( 8) hydrogen bonds : bond 0.09976 ( 1404) hydrogen bonds : angle 3.55270 ( 4104) metal coordination : bond 0.01988 ( 16) metal coordination : angle 8.97488 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 279 time to evaluate : 0.886 Fit side-chains REVERT: A 343 MET cc_start: 0.5115 (ttp) cc_final: 0.4864 (ttm) REVERT: C 343 MET cc_start: 0.5019 (ttp) cc_final: 0.4725 (ttm) REVERT: B 340 LEU cc_start: 0.7449 (mt) cc_final: 0.7238 (mt) REVERT: B 343 MET cc_start: 0.4992 (ttp) cc_final: 0.4688 (ttm) REVERT: D 340 LEU cc_start: 0.7447 (mt) cc_final: 0.7239 (mt) REVERT: D 343 MET cc_start: 0.4995 (ttp) cc_final: 0.4690 (ttm) outliers start: 8 outliers final: 6 residues processed: 287 average time/residue: 0.6068 time to fit residues: 197.9971 Evaluate side-chains 262 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 256 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 422 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 GLN A 533 ASN A 551 ASN C 386 GLN C 533 ASN B 533 ASN D 533 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.188448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143625 restraints weight = 24174.083| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.59 r_work: 0.3465 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22784 Z= 0.105 Angle : 0.463 6.231 30840 Z= 0.242 Chirality : 0.035 0.186 3468 Planarity : 0.004 0.037 3808 Dihedral : 12.149 170.685 3607 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.86 % Allowed : 18.07 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.17), residues: 2668 helix: 2.44 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 71 TYR 0.013 0.001 TYR A 524 PHE 0.018 0.001 PHE D 341 TRP 0.009 0.001 TRP A 315 HIS 0.003 0.000 HIS D 634 Details of bonding type rmsd covalent geometry : bond 0.00204 (22764) covalent geometry : angle 0.45977 (30820) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.49244 ( 8) hydrogen bonds : bond 0.04672 ( 1404) hydrogen bonds : angle 3.14762 ( 4104) metal coordination : bond 0.00740 ( 16) metal coordination : angle 2.58044 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 273 time to evaluate : 0.662 Fit side-chains REVERT: A 335 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7520 (mmt) REVERT: A 391 THR cc_start: 0.3626 (OUTLIER) cc_final: 0.3421 (p) REVERT: C 335 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7502 (mmt) REVERT: C 391 THR cc_start: 0.3546 (OUTLIER) cc_final: 0.3344 (p) REVERT: B 335 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7527 (mmt) REVERT: D 335 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7493 (mmt) REVERT: D 391 THR cc_start: 0.3429 (OUTLIER) cc_final: 0.3227 (p) outliers start: 89 outliers final: 26 residues processed: 329 average time/residue: 0.5851 time to fit residues: 219.3463 Evaluate side-chains 286 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 GLN Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 521 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 263 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 chunk 12 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 216 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN C 551 ASN B 533 ASN B 551 ASN D 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.186232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128568 restraints weight = 23980.931| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.01 r_work: 0.3425 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22784 Z= 0.124 Angle : 0.489 7.169 30840 Z= 0.253 Chirality : 0.036 0.218 3468 Planarity : 0.004 0.040 3808 Dihedral : 11.425 170.247 3598 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.99 % Allowed : 18.37 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.16), residues: 2668 helix: 2.57 (0.12), residues: 1940 sheet: None (None), residues: 0 loop : -1.22 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 71 TYR 0.016 0.001 TYR A 524 PHE 0.016 0.001 PHE B 341 TRP 0.013 0.001 TRP D 315 HIS 0.002 0.001 HIS A 271 Details of bonding type rmsd covalent geometry : bond 0.00264 (22764) covalent geometry : angle 0.48832 (30820) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.59281 ( 8) hydrogen bonds : bond 0.05584 ( 1404) hydrogen bonds : angle 3.18119 ( 4104) metal coordination : bond 0.00301 ( 16) metal coordination : angle 1.58023 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 269 time to evaluate : 0.760 Fit side-chains REVERT: A 186 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: A 335 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7453 (mmt) REVERT: A 339 PHE cc_start: 0.7428 (m-80) cc_final: 0.7187 (m-80) REVERT: A 383 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7182 (mp) REVERT: A 391 THR cc_start: 0.3652 (OUTLIER) cc_final: 0.3434 (p) REVERT: C 186 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: C 335 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7478 (mmt) REVERT: C 391 THR cc_start: 0.3501 (OUTLIER) cc_final: 0.3278 (p) REVERT: B 160 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8185 (tp) REVERT: B 335 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7486 (mmt) REVERT: B 339 PHE cc_start: 0.7449 (m-80) cc_final: 0.7210 (m-80) REVERT: D 160 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8168 (tp) REVERT: D 335 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7451 (mmt) REVERT: D 339 PHE cc_start: 0.7442 (m-80) cc_final: 0.7204 (m-80) REVERT: D 391 THR cc_start: 0.3479 (OUTLIER) cc_final: 0.3262 (p) outliers start: 92 outliers final: 25 residues processed: 339 average time/residue: 0.5098 time to fit residues: 199.5537 Evaluate side-chains 294 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 257 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 521 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 168 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 199 optimal weight: 20.0000 chunk 251 optimal weight: 0.0070 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 443 ASN A 533 ASN A 551 ASN C 154 ASN C 163 GLN C 443 ASN C 533 ASN C 551 ASN B 154 ASN B 551 ASN D 154 ASN D 443 ASN D 533 ASN D 551 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.180731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122391 restraints weight = 23870.393| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.00 r_work: 0.3341 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22784 Z= 0.254 Angle : 0.649 8.072 30840 Z= 0.332 Chirality : 0.043 0.219 3468 Planarity : 0.005 0.049 3808 Dihedral : 11.854 151.596 3598 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.42 % Allowed : 17.50 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.16), residues: 2668 helix: 2.12 (0.12), residues: 1948 sheet: None (None), residues: 0 loop : -1.18 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 71 TYR 0.021 0.002 TYR A 524 PHE 0.020 0.002 PHE B 237 TRP 0.018 0.002 TRP D 315 HIS 0.004 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00630 (22764) covalent geometry : angle 0.64734 (30820) SS BOND : bond 0.00718 ( 4) SS BOND : angle 1.62265 ( 8) hydrogen bonds : bond 0.08494 ( 1404) hydrogen bonds : angle 3.50694 ( 4104) metal coordination : bond 0.00526 ( 16) metal coordination : angle 1.85524 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 268 time to evaluate : 0.793 Fit side-chains REVERT: A 186 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: A 335 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7324 (mpp) REVERT: A 383 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7498 (mp) REVERT: A 391 THR cc_start: 0.3753 (OUTLIER) cc_final: 0.3535 (p) REVERT: A 521 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7836 (mp) REVERT: C 186 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: C 272 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7620 (ttt180) REVERT: C 335 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7326 (mpp) REVERT: C 383 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7492 (mp) REVERT: C 391 THR cc_start: 0.3719 (OUTLIER) cc_final: 0.3496 (p) REVERT: C 521 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7827 (mp) REVERT: B 186 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: B 272 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7636 (ttt180) REVERT: B 335 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7385 (mpp) REVERT: B 521 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7845 (mp) REVERT: B 551 ASN cc_start: 0.8033 (t160) cc_final: 0.7820 (t0) REVERT: D 335 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7363 (mpp) REVERT: D 383 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7461 (mp) REVERT: D 391 THR cc_start: 0.3635 (OUTLIER) cc_final: 0.3409 (p) REVERT: D 551 ASN cc_start: 0.8055 (t160) cc_final: 0.7851 (t0) outliers start: 125 outliers final: 50 residues processed: 353 average time/residue: 0.5159 time to fit residues: 210.6890 Evaluate side-chains 333 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 265 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 545 ARG Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 545 ARG Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 GLN Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 710 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 258 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 chunk 249 optimal weight: 0.9990 chunk 257 optimal weight: 0.8980 chunk 50 optimal weight: 30.0000 chunk 105 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 386 GLN A 551 ASN C 154 ASN C 386 GLN C 551 ASN B 154 ASN B 386 GLN D 154 ASN D 386 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.185821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128713 restraints weight = 23748.880| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.96 r_work: 0.3449 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22784 Z= 0.116 Angle : 0.496 8.323 30840 Z= 0.255 Chirality : 0.036 0.257 3468 Planarity : 0.004 0.042 3808 Dihedral : 11.101 154.743 3592 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.11 % Allowed : 18.33 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.16), residues: 2668 helix: 2.45 (0.12), residues: 1944 sheet: None (None), residues: 0 loop : -1.22 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 71 TYR 0.014 0.001 TYR D 524 PHE 0.013 0.001 PHE D 540 TRP 0.011 0.001 TRP C 315 HIS 0.002 0.000 HIS D 387 Details of bonding type rmsd covalent geometry : bond 0.00229 (22764) covalent geometry : angle 0.49549 (30820) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.46779 ( 8) hydrogen bonds : bond 0.05460 ( 1404) hydrogen bonds : angle 3.25802 ( 4104) metal coordination : bond 0.00374 ( 16) metal coordination : angle 1.51335 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 264 time to evaluate : 0.640 Fit side-chains REVERT: A 186 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: A 335 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7665 (mmm) REVERT: A 391 THR cc_start: 0.3576 (OUTLIER) cc_final: 0.3366 (p) REVERT: A 422 MET cc_start: 0.6555 (tmm) cc_final: 0.6250 (tmt) REVERT: A 521 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7808 (mp) REVERT: C 186 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: C 335 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7635 (mmm) REVERT: C 420 LYS cc_start: 0.7295 (mtpp) cc_final: 0.7019 (mtpp) REVERT: C 422 MET cc_start: 0.6762 (tmm) cc_final: 0.6428 (tmt) REVERT: C 521 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7777 (mp) REVERT: B 186 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: B 272 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7557 (ttt180) REVERT: B 335 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7694 (mmm) REVERT: B 383 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7234 (mp) REVERT: B 420 LYS cc_start: 0.7309 (mtpp) cc_final: 0.7033 (mtpp) REVERT: B 422 MET cc_start: 0.6746 (tmm) cc_final: 0.6429 (tmt) REVERT: B 521 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7809 (mp) REVERT: B 551 ASN cc_start: 0.7794 (t160) cc_final: 0.7477 (t0) REVERT: D 335 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7694 (mmm) REVERT: D 420 LYS cc_start: 0.7280 (mtpp) cc_final: 0.7004 (mtpp) REVERT: D 422 MET cc_start: 0.6772 (tmm) cc_final: 0.6452 (tmt) REVERT: D 521 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7839 (mp) REVERT: D 551 ASN cc_start: 0.7779 (t160) cc_final: 0.7458 (t0) outliers start: 118 outliers final: 37 residues processed: 347 average time/residue: 0.5381 time to fit residues: 215.3050 Evaluate side-chains 301 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 589 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 97 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 147 optimal weight: 0.0000 chunk 110 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 533 ASN A 551 ASN C 154 ASN C 533 ASN C 551 ASN B 154 ASN B 533 ASN B 551 ASN D 154 ASN D 533 ASN D 551 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.185441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127742 restraints weight = 23996.307| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.99 r_work: 0.3441 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22784 Z= 0.126 Angle : 0.499 7.877 30840 Z= 0.257 Chirality : 0.036 0.156 3468 Planarity : 0.004 0.041 3808 Dihedral : 10.886 153.106 3592 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.59 % Allowed : 19.24 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.16), residues: 2668 helix: 2.50 (0.12), residues: 1940 sheet: None (None), residues: 0 loop : -1.13 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 71 TYR 0.015 0.001 TYR D 524 PHE 0.013 0.001 PHE A 540 TRP 0.013 0.001 TRP B 315 HIS 0.002 0.001 HIS D 387 Details of bonding type rmsd covalent geometry : bond 0.00271 (22764) covalent geometry : angle 0.49807 (30820) SS BOND : bond 0.00232 ( 4) SS BOND : angle 0.65346 ( 8) hydrogen bonds : bond 0.05757 ( 1404) hydrogen bonds : angle 3.23768 ( 4104) metal coordination : bond 0.00364 ( 16) metal coordination : angle 1.22802 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 264 time to evaluate : 0.890 Fit side-chains REVERT: A 186 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: A 335 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7300 (mpp) REVERT: A 420 LYS cc_start: 0.7340 (ttpp) cc_final: 0.7135 (mtpp) REVERT: A 422 MET cc_start: 0.6580 (tmm) cc_final: 0.6294 (tmt) REVERT: A 467 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: A 521 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7789 (mp) REVERT: C 186 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: C 335 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7276 (mpp) REVERT: C 420 LYS cc_start: 0.7294 (mtpp) cc_final: 0.6982 (mtpp) REVERT: C 422 MET cc_start: 0.6834 (tmm) cc_final: 0.6451 (ttt) REVERT: C 467 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: C 521 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7790 (mp) REVERT: B 186 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: B 272 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7591 (ttt180) REVERT: B 335 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7381 (mpp) REVERT: B 383 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7257 (mp) REVERT: B 420 LYS cc_start: 0.7293 (mtpp) cc_final: 0.6983 (mtpp) REVERT: B 422 MET cc_start: 0.6819 (tmm) cc_final: 0.6439 (ttt) REVERT: B 521 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7803 (mp) REVERT: B 551 ASN cc_start: 0.7858 (t0) cc_final: 0.7510 (t0) REVERT: D 335 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7375 (mpp) REVERT: D 383 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7267 (mp) REVERT: D 420 LYS cc_start: 0.7268 (mtpp) cc_final: 0.6956 (mtpp) REVERT: D 422 MET cc_start: 0.6834 (tmm) cc_final: 0.6451 (ttt) REVERT: D 521 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7852 (mp) REVERT: D 551 ASN cc_start: 0.7858 (t0) cc_final: 0.7517 (t0) outliers start: 106 outliers final: 51 residues processed: 342 average time/residue: 0.5750 time to fit residues: 225.6059 Evaluate side-chains 324 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 257 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 304 GLN Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 589 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 247 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 163 GLN A 551 ASN C 154 ASN C 551 ASN B 154 ASN B 163 GLN D 154 ASN D 163 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128868 restraints weight = 23876.151| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.10 r_work: 0.3428 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 22784 Z= 0.120 Angle : 0.495 9.049 30840 Z= 0.253 Chirality : 0.037 0.284 3468 Planarity : 0.004 0.043 3808 Dihedral : 10.692 152.703 3592 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.59 % Allowed : 18.93 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.16), residues: 2668 helix: 2.47 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -1.20 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 71 TYR 0.015 0.001 TYR D 524 PHE 0.013 0.001 PHE B 540 TRP 0.013 0.001 TRP B 315 HIS 0.002 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00254 (22764) covalent geometry : angle 0.49428 (30820) SS BOND : bond 0.00178 ( 4) SS BOND : angle 0.54145 ( 8) hydrogen bonds : bond 0.05438 ( 1404) hydrogen bonds : angle 3.21937 ( 4104) metal coordination : bond 0.00294 ( 16) metal coordination : angle 1.23025 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 267 time to evaluate : 0.919 Fit side-chains REVERT: A 186 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: A 335 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7303 (mpp) REVERT: A 383 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7194 (mp) REVERT: A 422 MET cc_start: 0.6674 (tmm) cc_final: 0.6424 (tmt) REVERT: C 186 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: C 272 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7539 (ttt180) REVERT: C 335 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7246 (mpp) REVERT: C 383 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7198 (mp) REVERT: C 420 LYS cc_start: 0.7162 (mtpp) cc_final: 0.6923 (mtpp) REVERT: C 422 MET cc_start: 0.6832 (tmm) cc_final: 0.6445 (ttt) REVERT: C 467 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: C 521 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7732 (mp) REVERT: B 186 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: B 272 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7567 (ttt180) REVERT: B 335 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7362 (mpp) REVERT: B 383 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7193 (mp) REVERT: B 420 LYS cc_start: 0.7165 (mtpp) cc_final: 0.6930 (mtpp) REVERT: B 422 MET cc_start: 0.6810 (tmm) cc_final: 0.6428 (ttt) REVERT: B 467 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: B 521 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7707 (mp) REVERT: B 551 ASN cc_start: 0.7808 (t0) cc_final: 0.7437 (t0) REVERT: D 335 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7353 (mpp) REVERT: D 383 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7182 (mp) REVERT: D 420 LYS cc_start: 0.7129 (mtpp) cc_final: 0.6890 (mtpp) REVERT: D 422 MET cc_start: 0.6819 (tmm) cc_final: 0.6433 (ttt) REVERT: D 521 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7816 (mp) REVERT: D 551 ASN cc_start: 0.7799 (t0) cc_final: 0.7440 (t0) outliers start: 106 outliers final: 51 residues processed: 327 average time/residue: 0.5873 time to fit residues: 219.9987 Evaluate side-chains 325 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 256 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 GLN Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 589 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 184 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 258 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 214 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN D 154 ASN D 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.187301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129819 restraints weight = 23821.048| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.01 r_work: 0.3460 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22784 Z= 0.110 Angle : 0.479 9.448 30840 Z= 0.246 Chirality : 0.036 0.176 3468 Planarity : 0.004 0.047 3808 Dihedral : 10.447 152.914 3592 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.42 % Allowed : 19.97 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.16), residues: 2668 helix: 2.53 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -1.18 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 71 TYR 0.014 0.001 TYR A 524 PHE 0.013 0.001 PHE B 540 TRP 0.012 0.001 TRP B 315 HIS 0.001 0.000 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00223 (22764) covalent geometry : angle 0.47881 (30820) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.49726 ( 8) hydrogen bonds : bond 0.04936 ( 1404) hydrogen bonds : angle 3.16514 ( 4104) metal coordination : bond 0.00328 ( 16) metal coordination : angle 1.06639 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 268 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8003 (tt) REVERT: A 335 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7304 (mpp) REVERT: A 422 MET cc_start: 0.6610 (tmm) cc_final: 0.6364 (ttt) REVERT: A 467 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: C 272 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7537 (ttt180) REVERT: C 335 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7671 (mmm) REVERT: C 420 LYS cc_start: 0.7068 (mtpp) cc_final: 0.6781 (mtpp) REVERT: C 422 MET cc_start: 0.6801 (tmm) cc_final: 0.6418 (ttt) REVERT: C 467 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: B 272 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7545 (ttt180) REVERT: B 335 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7309 (mpp) REVERT: B 420 LYS cc_start: 0.7073 (mtpp) cc_final: 0.6789 (mtpp) REVERT: B 422 MET cc_start: 0.6785 (tmm) cc_final: 0.6406 (ttt) REVERT: B 467 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: B 551 ASN cc_start: 0.7783 (t0) cc_final: 0.7424 (t0) REVERT: D 335 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7295 (mpp) REVERT: D 383 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7211 (mp) REVERT: D 420 LYS cc_start: 0.7048 (mtpp) cc_final: 0.6759 (mtpp) REVERT: D 422 MET cc_start: 0.6799 (tmm) cc_final: 0.6418 (ttt) REVERT: D 467 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: D 551 ASN cc_start: 0.7768 (t0) cc_final: 0.7414 (t0) outliers start: 79 outliers final: 50 residues processed: 315 average time/residue: 0.5972 time to fit residues: 215.3350 Evaluate side-chains 316 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 589 ASN Chi-restraints excluded: chain D residue 710 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 112 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 216 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 551 ASN C 533 ASN C 551 ASN B 154 ASN B 443 ASN B 533 ASN D 154 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.183087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.125055 restraints weight = 23896.711| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.01 r_work: 0.3393 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22784 Z= 0.176 Angle : 0.576 9.665 30840 Z= 0.292 Chirality : 0.040 0.281 3468 Planarity : 0.004 0.045 3808 Dihedral : 10.916 148.129 3592 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.73 % Allowed : 19.28 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.16), residues: 2668 helix: 2.32 (0.12), residues: 1960 sheet: None (None), residues: 0 loop : -1.25 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 71 TYR 0.017 0.001 TYR A 524 PHE 0.014 0.002 PHE C 301 TRP 0.014 0.001 TRP B 315 HIS 0.003 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00418 (22764) covalent geometry : angle 0.57526 (30820) SS BOND : bond 0.00450 ( 4) SS BOND : angle 0.92321 ( 8) hydrogen bonds : bond 0.06989 ( 1404) hydrogen bonds : angle 3.35660 ( 4104) metal coordination : bond 0.00452 ( 16) metal coordination : angle 1.46671 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 251 time to evaluate : 0.924 Fit side-chains REVERT: A 335 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7312 (mpp) REVERT: A 422 MET cc_start: 0.6753 (tmm) cc_final: 0.6452 (ttt) REVERT: A 521 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7795 (mp) REVERT: C 272 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7573 (ttt180) REVERT: C 335 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7327 (mpp) REVERT: C 383 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7271 (mp) REVERT: C 422 MET cc_start: 0.6814 (tmm) cc_final: 0.6418 (ttt) REVERT: C 521 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7787 (mp) REVERT: B 154 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8563 (t0) REVERT: B 272 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7587 (ttt180) REVERT: B 335 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7337 (mpp) REVERT: B 420 LYS cc_start: 0.7100 (mtpp) cc_final: 0.6838 (mtpp) REVERT: B 422 MET cc_start: 0.6791 (tmm) cc_final: 0.6402 (ttt) REVERT: B 467 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: B 521 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7801 (mp) REVERT: B 551 ASN cc_start: 0.7879 (t0) cc_final: 0.7482 (t0) REVERT: D 335 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7339 (mpp) REVERT: D 383 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7261 (mp) REVERT: D 420 LYS cc_start: 0.7117 (mtpp) cc_final: 0.6850 (mtpp) REVERT: D 422 MET cc_start: 0.6807 (tmm) cc_final: 0.6416 (ttt) REVERT: D 467 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: D 521 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7826 (mp) REVERT: D 551 ASN cc_start: 0.7867 (t0) cc_final: 0.7479 (t0) outliers start: 86 outliers final: 62 residues processed: 311 average time/residue: 0.5866 time to fit residues: 209.6995 Evaluate side-chains 331 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 254 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 GLN Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 589 ASN Chi-restraints excluded: chain D residue 710 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 191 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 233 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.185935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.128259 restraints weight = 24062.045| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.02 r_work: 0.3440 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22784 Z= 0.124 Angle : 0.514 10.079 30840 Z= 0.263 Chirality : 0.037 0.263 3468 Planarity : 0.004 0.047 3808 Dihedral : 10.651 149.597 3592 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.38 % Allowed : 19.89 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.16), residues: 2668 helix: 2.46 (0.12), residues: 1960 sheet: None (None), residues: 0 loop : -1.21 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 71 TYR 0.015 0.001 TYR A 524 PHE 0.013 0.001 PHE C 341 TRP 0.013 0.001 TRP C 315 HIS 0.003 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00261 (22764) covalent geometry : angle 0.51376 (30820) SS BOND : bond 0.00138 ( 4) SS BOND : angle 0.41930 ( 8) hydrogen bonds : bond 0.05448 ( 1404) hydrogen bonds : angle 3.26761 ( 4104) metal coordination : bond 0.00381 ( 16) metal coordination : angle 1.32313 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 256 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7290 (mpp) REVERT: A 422 MET cc_start: 0.6740 (tmm) cc_final: 0.6446 (ttt) REVERT: A 521 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7679 (mp) REVERT: C 272 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7564 (ttt180) REVERT: C 335 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7312 (mpp) REVERT: C 422 MET cc_start: 0.6800 (tmm) cc_final: 0.6430 (ttt) REVERT: C 520 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: C 521 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7689 (mp) REVERT: B 272 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7554 (ttt180) REVERT: B 335 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7325 (mpp) REVERT: B 422 MET cc_start: 0.6777 (tmm) cc_final: 0.6422 (ttt) REVERT: B 467 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: B 521 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7715 (mp) REVERT: B 551 ASN cc_start: 0.7790 (t0) cc_final: 0.7417 (t0) REVERT: D 335 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7331 (mpp) REVERT: D 422 MET cc_start: 0.6794 (tmm) cc_final: 0.6435 (ttt) REVERT: D 467 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: D 521 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7746 (mp) REVERT: D 551 ASN cc_start: 0.7765 (t0) cc_final: 0.7403 (t0) outliers start: 78 outliers final: 48 residues processed: 305 average time/residue: 0.6294 time to fit residues: 219.2833 Evaluate side-chains 310 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 249 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 GLN Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 589 ASN Chi-restraints excluded: chain D residue 710 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 chunk 213 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN D 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.183635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125784 restraints weight = 23831.975| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.00 r_work: 0.3400 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22784 Z= 0.163 Angle : 0.562 10.409 30840 Z= 0.286 Chirality : 0.039 0.276 3468 Planarity : 0.004 0.044 3808 Dihedral : 10.840 147.204 3592 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.03 % Allowed : 20.15 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.16), residues: 2668 helix: 2.34 (0.12), residues: 1960 sheet: None (None), residues: 0 loop : -1.18 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 71 TYR 0.017 0.001 TYR C 524 PHE 0.013 0.002 PHE C 341 TRP 0.014 0.001 TRP C 315 HIS 0.003 0.001 HIS A 271 Details of bonding type rmsd covalent geometry : bond 0.00383 (22764) covalent geometry : angle 0.56132 (30820) SS BOND : bond 0.00388 ( 4) SS BOND : angle 0.83872 ( 8) hydrogen bonds : bond 0.06542 ( 1404) hydrogen bonds : angle 3.33758 ( 4104) metal coordination : bond 0.00502 ( 16) metal coordination : angle 1.45326 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9276.55 seconds wall clock time: 157 minutes 51.27 seconds (9471.27 seconds total)