Starting phenix.real_space_refine on Sat Jul 4 18:49:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khj_62344/07_2026/9khj_62344.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khj_62344/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9khj_62344/07_2026/9khj_62344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khj_62344/07_2026/9khj_62344.map" model { file = "/net/cci-nas-00/data/ceres_data/9khj_62344/07_2026/9khj_62344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khj_62344/07_2026/9khj_62344.cif" } 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-dev-6108/lib/python3.11/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, 156 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 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, 156 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 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, 156 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 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, 156 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 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: 4.33, per 1000 atoms: 0.19 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: 1.75 Conformation dependent library (CDL) restraints added in 1.0 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: 0.57 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: 3.54 Time building geometry restraints manager: 2.34 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: 0.07 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: 2.950 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: 0.460 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.370 Find NCS groups from input model: 0.200 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:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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/Z covalent geometry : bond 0.00477 / 0.29 (22764) covalent geometry : angle 0.72756 / 0.41 (30820) SS BOND : bond 0.00180 / 0.09 ( 4) SS BOND : angle 0.39162 / 0.25 ( 8) hydrogen bonds : bond 0.09976 / 7.11 ( 1404) hydrogen bonds : angle 3.55270 / 2.54 ( 4104) metal coordination : bond 0.01988 / 1.30 ( 16) metal coordination : angle 8.97488 / 5.83 ( 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 : 0.882 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: 0.5876 time to fit residues: 193.5691 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 : 0.786 ------------------------------------------------------------------------------- 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... A 386 GLN A 533 ASN A 551 ASN C 386 GLN C 533 ASN C 551 ASN B 533 ASN D 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.188383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143395 restraints weight = 24168.033| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.61 r_work: 0.3447 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22784 Z= 0.108 Angle : 0.464 6.237 30840 Z= 0.242 Chirality : 0.035 0.186 3468 Planarity : 0.004 0.037 3808 Dihedral : 12.257 170.103 3607 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.77 % Allowed : 18.33 % Favored : 77.90 % 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 0.008 0.000 ARG C 71 TYR 0.013 0.001 TYR A 524 PHE 0.019 0.001 PHE D 341 TRP 0.009 0.001 TRP A 315 HIS 0.002 0.000 HIS D 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.11 (22764) covalent geometry : angle 0.45985 / 0.24 (30820) SS BOND : bond 0.00089 / 0.04 ( 4) SS BOND : angle 0.46894 / 0.27 ( 8) hydrogen bonds : bond 0.04765 / 3.25 ( 1404) hydrogen bonds : angle 3.16357 / 2.28 ( 4104) metal coordination : bond 0.00679 / 0.53 ( 16) metal coordination : angle 3.05914 / 1.99 ( 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 361 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 274 time to evaluate : 0.905 Fit side-chains REVERT: A 335 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7466 (mmt) REVERT: A 391 THR cc_start: 0.3626 (OUTLIER) cc_final: 0.3425 (p) REVERT: C 335 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7492 (mmt) REVERT: C 391 THR cc_start: 0.3590 (OUTLIER) cc_final: 0.3386 (p) REVERT: B 335 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7489 (mmt) REVERT: D 335 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7467 (mmt) outliers start: 87 outliers final: 23 residues processed: 329 average time/residue: 0.5884 time to fit residues: 222.9890 Evaluate side-chains 287 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 258 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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 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 335 MET Chi-restraints excluded: chain D residue 341 PHE 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: 2.9990 chunk 36 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 248 optimal weight: 0.4980 chunk 68 optimal weight: 20.0000 chunk 29 optimal weight: 0.0970 chunk 12 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 551 ASN B 551 ASN D 551 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.184149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126674 restraints weight = 23864.414| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.09 r_work: 0.3389 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22784 Z= 0.157 Angle : 0.538 6.794 30840 Z= 0.277 Chirality : 0.038 0.214 3468 Planarity : 0.004 0.043 3808 Dihedral : 11.633 165.850 3598 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.38 % Allowed : 17.98 % 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: 2.27 (0.16), residues: 2668 helix: 2.41 (0.12), residues: 1948 sheet: None (None), residues: 0 loop : -1.12 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 71 TYR 0.018 0.001 TYR A 524 PHE 0.015 0.002 PHE C 341 TRP 0.014 0.001 TRP B 315 HIS 0.002 0.001 HIS C 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (22764) covalent geometry : angle 0.53698 / 0.28 (30820) SS BOND : bond 0.00347 / 0.17 ( 4) SS BOND : angle 0.91457 / 0.58 ( 8) hydrogen bonds : bond 0.06633 / 4.48 ( 1404) hydrogen bonds : angle 3.30480 / 2.38 ( 4104) metal coordination : bond 0.00344 / 0.24 ( 16) metal coordination : angle 1.84618 / 1.12 ( 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 360 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 259 time to evaluate : 0.704 Fit side-chains REVERT: A 186 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: A 383 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7186 (mp) REVERT: A 391 THR cc_start: 0.3744 (OUTLIER) cc_final: 0.3523 (p) REVERT: A 494 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8118 (mt) REVERT: A 551 ASN cc_start: 0.7791 (t160) cc_final: 0.7555 (t0) REVERT: C 186 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: C 272 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7553 (ttt180) REVERT: C 335 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7594 (mmm) REVERT: C 339 PHE cc_start: 0.7413 (m-80) cc_final: 0.7151 (m-80) REVERT: C 391 THR cc_start: 0.3676 (OUTLIER) cc_final: 0.3453 (p) REVERT: C 494 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8123 (mt) REVERT: C 521 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7620 (mp) REVERT: B 160 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8204 (tp) REVERT: B 335 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7629 (mmm) REVERT: B 339 PHE cc_start: 0.7457 (m-80) cc_final: 0.7219 (m-80) REVERT: B 343 MET cc_start: 0.5302 (ttp) cc_final: 0.5030 (ttm) REVERT: B 494 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8112 (mt) REVERT: B 521 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7639 (mp) REVERT: B 551 ASN cc_start: 0.7777 (t0) cc_final: 0.7568 (t0) REVERT: D 160 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8195 (tp) REVERT: D 335 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7622 (mmm) REVERT: D 339 PHE cc_start: 0.7469 (m-80) cc_final: 0.7260 (m-80) REVERT: D 343 MET cc_start: 0.5300 (ttp) cc_final: 0.5030 (ttm) REVERT: D 494 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8118 (mt) REVERT: D 521 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7629 (mp) REVERT: D 551 ASN cc_start: 0.7788 (t0) cc_final: 0.7573 (t0) outliers start: 101 outliers final: 34 residues processed: 330 average time/residue: 0.5711 time to fit residues: 217.1965 Evaluate side-chains 302 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 250 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 167 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 GLN 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 494 ILE 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 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 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 391 THR Chi-restraints excluded: chain C residue 494 ILE 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 190 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 494 ILE 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 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 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 494 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 544 THR 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: 6.9990 chunk 61 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 251 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 551 ASN C 163 GLN C 551 ASN B 154 ASN B 163 GLN D 154 ASN D 163 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.184629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126586 restraints weight = 23854.272| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.02 r_work: 0.3415 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22784 Z= 0.141 Angle : 0.512 7.255 30840 Z= 0.266 Chirality : 0.038 0.235 3468 Planarity : 0.004 0.042 3808 Dihedral : 11.294 158.436 3598 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.24 % Allowed : 17.68 % 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: 2.25 (0.16), residues: 2668 helix: 2.44 (0.12), residues: 1940 sheet: None (None), residues: 0 loop : -1.25 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 71 TYR 0.017 0.001 TYR C 524 PHE 0.016 0.001 PHE D 341 TRP 0.013 0.001 TRP D 315 HIS 0.002 0.001 HIS A 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (22764) covalent geometry : angle 0.51156 / 0.27 (30820) SS BOND : bond 0.00280 / 0.14 ( 4) SS BOND : angle 0.72124 / 0.44 ( 8) hydrogen bonds : bond 0.06148 / 4.17 ( 1404) hydrogen bonds : angle 3.28356 / 2.36 ( 4104) metal coordination : bond 0.00445 / 0.35 ( 16) metal coordination : angle 1.57955 / 0.99 ( 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 384 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 263 time to evaluate : 0.853 Fit side-chains REVERT: A 186 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: A 383 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7286 (mp) REVERT: A 391 THR cc_start: 0.3629 (OUTLIER) cc_final: 0.3409 (p) REVERT: A 521 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7728 (mp) REVERT: A 551 ASN cc_start: 0.7815 (t0) cc_final: 0.7502 (t0) REVERT: C 186 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: C 272 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7594 (ttt180) REVERT: C 335 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7285 (mpp) REVERT: C 383 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7270 (mp) REVERT: C 391 THR cc_start: 0.3593 (OUTLIER) cc_final: 0.3373 (p) REVERT: C 521 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7773 (mp) REVERT: B 160 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8295 (tp) REVERT: B 186 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: B 335 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7725 (mmm) REVERT: B 383 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7225 (mp) REVERT: B 521 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7798 (mp) REVERT: B 551 ASN cc_start: 0.7859 (t0) cc_final: 0.7542 (t0) REVERT: D 160 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8303 (tp) REVERT: D 335 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7706 (mmm) REVERT: D 383 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7217 (mp) REVERT: D 521 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7795 (mp) REVERT: D 551 ASN cc_start: 0.7852 (t0) cc_final: 0.7539 (t0) outliers start: 121 outliers final: 45 residues processed: 343 average time/residue: 0.5264 time to fit residues: 209.9375 Evaluate side-chains 315 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 251 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 GLN 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 447 LEU 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 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 391 THR 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 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 184 SER Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 235 ASN 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 383 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 589 ASN 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 184 SER 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 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 447 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 589 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 258 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 249 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 50 optimal weight: 0.0010 chunk 105 optimal weight: 30.0000 chunk 126 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN C 154 ASN C 551 ASN B 154 ASN B 533 ASN D 154 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 = 0.4149 r_free = 0.4149 target = 0.187121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129504 restraints weight = 23751.375| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.00 r_work: 0.3458 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22784 Z= 0.110 Angle : 0.476 8.531 30840 Z= 0.245 Chirality : 0.036 0.208 3468 Planarity : 0.004 0.039 3808 Dihedral : 10.838 157.595 3598 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.94 % Allowed : 18.02 % Favored : 77.04 % 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: 2.50 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 71 TYR 0.014 0.001 TYR A 524 PHE 0.016 0.001 PHE B 341 TRP 0.012 0.001 TRP D 315 HIS 0.001 0.000 HIS D 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (22764) covalent geometry : angle 0.47588 / 0.25 (30820) SS BOND : bond 0.00097 / 0.05 ( 4) SS BOND : angle 0.37274 / 0.22 ( 8) hydrogen bonds : bond 0.05057 / 3.44 ( 1404) hydrogen bonds : angle 3.17847 / 2.28 ( 4104) metal coordination : bond 0.00321 / 0.25 ( 16) metal coordination : angle 1.32293 / 0.82 ( 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 377 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 263 time to evaluate : 0.814 Fit side-chains REVERT: A 186 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: A 335 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7578 (mmt) REVERT: A 383 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7161 (mp) REVERT: A 391 THR cc_start: 0.3607 (OUTLIER) cc_final: 0.3393 (p) REVERT: A 442 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7296 (ttm) REVERT: A 551 ASN cc_start: 0.7752 (t0) cc_final: 0.7431 (t0) REVERT: C 186 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: C 335 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7699 (mmm) REVERT: C 391 THR cc_start: 0.3557 (OUTLIER) cc_final: 0.3341 (p) REVERT: C 420 LYS cc_start: 0.7364 (ttpp) cc_final: 0.7052 (mtpp) REVERT: C 442 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7319 (ttm) REVERT: C 467 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: B 186 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: B 335 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7697 (mmm) REVERT: B 442 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7345 (ttm) REVERT: B 521 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7728 (tp) REVERT: B 551 ASN cc_start: 0.7837 (t0) cc_final: 0.7484 (t0) REVERT: D 335 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7686 (mmm) REVERT: D 383 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7221 (mp) REVERT: D 442 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7348 (ttm) REVERT: D 521 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7722 (tp) REVERT: D 551 ASN cc_start: 0.7832 (t0) cc_final: 0.7464 (t0) outliers start: 114 outliers final: 41 residues processed: 339 average time/residue: 0.5629 time to fit residues: 220.6722 Evaluate side-chains 307 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 391 THR Chi-restraints excluded: chain A residue 442 MET 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 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 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 442 MET Chi-restraints excluded: chain C residue 467 GLU 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 140 THR Chi-restraints excluded: chain B residue 184 SER 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 335 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 442 MET 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 61 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 184 SER 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 442 MET Chi-restraints excluded: chain D residue 467 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 97 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 443 ASN A 533 ASN C 154 ASN C 443 ASN C 533 ASN C 551 ASN B 154 ASN D 154 ASN D 443 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.181524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123155 restraints weight = 23894.701| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.00 r_work: 0.3367 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22784 Z= 0.221 Angle : 0.627 8.124 30840 Z= 0.317 Chirality : 0.042 0.244 3468 Planarity : 0.005 0.045 3808 Dihedral : 11.514 149.081 3598 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.55 % Allowed : 17.68 % Favored : 76.78 % 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: 1.97 (0.16), residues: 2668 helix: 2.17 (0.12), residues: 1944 sheet: None (None), residues: 0 loop : -1.17 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 71 TYR 0.020 0.002 TYR B 524 PHE 0.019 0.002 PHE B 237 TRP 0.020 0.002 TRP D 423 HIS 0.004 0.001 HIS C 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (22764) covalent geometry : angle 0.62542 / 0.32 (30820) SS BOND : bond 0.00617 / 0.31 ( 4) SS BOND : angle 1.34014 / 0.84 ( 8) hydrogen bonds : bond 0.08064 / 5.43 ( 1404) hydrogen bonds : angle 3.48835 / 2.51 ( 4104) metal coordination : bond 0.00491 / 0.38 ( 16) metal coordination : angle 1.73943 / 1.13 ( 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 393 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 265 time to evaluate : 0.926 Fit side-chains REVERT: A 186 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: A 383 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7387 (mp) REVERT: A 391 THR cc_start: 0.3726 (OUTLIER) cc_final: 0.3514 (p) REVERT: A 521 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7782 (mp) REVERT: A 551 ASN cc_start: 0.7900 (t0) cc_final: 0.7515 (t0) REVERT: C 186 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: C 272 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7556 (ttt180) REVERT: C 335 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7305 (mpp) REVERT: C 341 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7701 (p90) REVERT: C 391 THR cc_start: 0.3705 (OUTLIER) cc_final: 0.3491 (p) REVERT: C 420 LYS cc_start: 0.7394 (ttpp) cc_final: 0.7170 (mtpp) REVERT: C 521 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7784 (mp) REVERT: B 160 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8397 (tp) REVERT: B 186 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: B 335 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7332 (mpp) REVERT: B 383 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7408 (mp) REVERT: B 420 LYS cc_start: 0.7401 (ttpp) cc_final: 0.7201 (mtpp) REVERT: B 521 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7786 (mp) REVERT: B 551 ASN cc_start: 0.7936 (t0) cc_final: 0.7532 (t0) REVERT: D 160 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8390 (tp) REVERT: D 335 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7325 (mpp) REVERT: D 383 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7410 (mp) REVERT: D 420 LYS cc_start: 0.7412 (ttpp) cc_final: 0.7212 (mtpp) REVERT: D 521 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7801 (mp) REVERT: D 551 ASN cc_start: 0.7918 (t0) cc_final: 0.7519 (t0) outliers start: 128 outliers final: 58 residues processed: 354 average time/residue: 0.5197 time to fit residues: 212.9614 Evaluate side-chains 337 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 260 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 190 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 383 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 515 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 545 ARG 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 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 190 LEU 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 272 ARG 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 470 GLU 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 140 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 235 ASN 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 343 MET Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 516 ASP 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 545 ARG 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 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 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 343 MET Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 516 ASP 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 545 ARG Chi-restraints excluded: chain D residue 710 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.185522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127864 restraints weight = 23816.748| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.97 r_work: 0.3440 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22784 Z= 0.124 Angle : 0.518 8.951 30840 Z= 0.263 Chirality : 0.037 0.221 3468 Planarity : 0.004 0.042 3808 Dihedral : 11.021 152.094 3598 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.46 % Allowed : 18.98 % 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: 2.23 (0.16), residues: 2668 helix: 2.38 (0.12), residues: 1960 sheet: None (None), residues: 0 loop : -1.23 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 71 TYR 0.015 0.001 TYR B 524 PHE 0.015 0.001 PHE C 341 TRP 0.013 0.001 TRP D 315 HIS 0.002 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (22764) covalent geometry : angle 0.51738 / 0.26 (30820) SS BOND : bond 0.00148 / 0.07 ( 4) SS BOND : angle 0.54032 / 0.32 ( 8) hydrogen bonds : bond 0.05612 / 3.81 ( 1404) hydrogen bonds : angle 3.30646 / 2.37 ( 4104) metal coordination : bond 0.00327 / 0.26 ( 16) metal coordination : angle 1.41885 / 0.89 ( 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 369 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 266 time to evaluate : 0.864 Fit side-chains REVERT: A 186 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: A 420 LYS cc_start: 0.7329 (ttpp) cc_final: 0.7090 (mtpp) REVERT: A 422 MET cc_start: 0.6601 (tmm) cc_final: 0.6313 (tmt) REVERT: A 467 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: A 521 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7731 (mp) REVERT: A 551 ASN cc_start: 0.7831 (t0) cc_final: 0.7466 (t0) REVERT: C 186 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: C 335 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7280 (mpp) REVERT: C 391 THR cc_start: 0.3552 (OUTLIER) cc_final: 0.3352 (p) REVERT: C 422 MET cc_start: 0.6579 (tmm) cc_final: 0.6282 (tmt) REVERT: C 521 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7783 (mp) REVERT: B 160 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8221 (tp) REVERT: B 186 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: B 335 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7328 (mpp) REVERT: B 422 MET cc_start: 0.6556 (tmm) cc_final: 0.6258 (tmt) REVERT: B 521 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7749 (mp) REVERT: B 551 ASN cc_start: 0.7841 (t0) cc_final: 0.7483 (t0) REVERT: D 160 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8218 (tp) REVERT: D 335 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7265 (mpp) REVERT: D 422 MET cc_start: 0.6573 (tmm) cc_final: 0.6275 (tmt) REVERT: D 521 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7777 (mp) REVERT: D 551 ASN cc_start: 0.7847 (t0) cc_final: 0.7485 (t0) outliers start: 103 outliers final: 48 residues processed: 333 average time/residue: 0.5367 time to fit residues: 206.5017 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 : 0.802 ------------------------------------------------------------------------------- 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 184 SER 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 341 PHE Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 THR 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 186 GLU Chi-restraints excluded: chain C residue 235 ASN 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 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 710 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 184 SER Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 235 ASN 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 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 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 184 SER 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 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 544 THR Chi-restraints excluded: chain D residue 710 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: 3.9990 chunk 99 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 258 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN C 154 ASN C 386 GLN C 551 ASN B 154 ASN B 533 ASN D 154 ASN D 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.183265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125151 restraints weight = 23836.501| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.00 r_work: 0.3400 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22784 Z= 0.167 Angle : 0.578 9.184 30840 Z= 0.290 Chirality : 0.039 0.224 3468 Planarity : 0.004 0.043 3808 Dihedral : 11.174 148.889 3598 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.29 % Allowed : 19.11 % 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: 2.15 (0.16), residues: 2668 helix: 2.35 (0.12), residues: 1936 sheet: None (None), residues: 0 loop : -1.21 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 71 TYR 0.016 0.001 TYR B 524 PHE 0.015 0.002 PHE B 341 TRP 0.015 0.002 TRP D 315 HIS 0.003 0.001 HIS C 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (22764) covalent geometry : angle 0.57691 / 0.29 (30820) SS BOND : bond 0.00414 / 0.21 ( 4) SS BOND : angle 0.97910 / 0.61 ( 8) hydrogen bonds : bond 0.06798 / 4.59 ( 1404) hydrogen bonds : angle 3.40826 / 2.45 ( 4104) metal coordination : bond 0.00462 / 0.37 ( 16) metal coordination : angle 1.45098 / 0.94 ( 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 368 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 269 time to evaluate : 0.855 Fit side-chains REVERT: A 420 LYS cc_start: 0.7369 (ttpp) cc_final: 0.7157 (mtpp) REVERT: A 422 MET cc_start: 0.6552 (tmm) cc_final: 0.6256 (tmt) REVERT: A 467 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7609 (pm20) REVERT: A 521 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7796 (mp) REVERT: A 551 ASN cc_start: 0.7893 (t0) cc_final: 0.7517 (t0) REVERT: C 272 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7558 (ttt180) REVERT: C 335 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7290 (mpp) REVERT: C 391 THR cc_start: 0.3673 (OUTLIER) cc_final: 0.3451 (p) REVERT: C 422 MET cc_start: 0.6627 (tmm) cc_final: 0.6335 (tmt) REVERT: C 521 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7812 (mp) REVERT: B 160 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8337 (tp) REVERT: B 186 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: B 335 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7316 (mpp) REVERT: B 422 MET cc_start: 0.6608 (tmm) cc_final: 0.6319 (tmt) REVERT: B 521 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7798 (mp) REVERT: B 551 ASN cc_start: 0.7898 (t0) cc_final: 0.7518 (t0) REVERT: D 160 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8332 (tp) REVERT: D 335 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7303 (mpp) REVERT: D 422 MET cc_start: 0.6630 (tmm) cc_final: 0.6339 (tmt) REVERT: D 521 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7815 (mp) REVERT: D 551 ASN cc_start: 0.7900 (t0) cc_final: 0.7523 (t0) outliers start: 99 outliers final: 64 residues processed: 345 average time/residue: 0.5589 time to fit residues: 222.3793 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 : 0.895 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 184 SER 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 341 PHE Chi-restraints excluded: chain A residue 467 GLU 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 545 ARG 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 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 253 LYS 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 391 THR 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 98 ASP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 186 GLU 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 304 GLN Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 407 ILE 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 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 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: 5.9990 chunk 151 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN C 154 ASN C 386 GLN C 551 ASN B 154 ASN D 154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.183501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125472 restraints weight = 23949.701| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.99 r_work: 0.3402 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22784 Z= 0.161 Angle : 0.578 9.824 30840 Z= 0.291 Chirality : 0.039 0.252 3468 Planarity : 0.004 0.043 3808 Dihedral : 11.213 148.280 3598 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.33 % Allowed : 19.28 % Favored : 76.39 % 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: 2.08 (0.16), residues: 2668 helix: 2.27 (0.12), residues: 1960 sheet: None (None), residues: 0 loop : -1.29 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 71 TYR 0.017 0.001 TYR A 524 PHE 0.015 0.002 PHE B 341 TRP 0.014 0.001 TRP D 315 HIS 0.002 0.001 HIS D 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (22764) covalent geometry : angle 0.57719 / 0.29 (30820) SS BOND : bond 0.00372 / 0.19 ( 4) SS BOND : angle 0.88658 / 0.55 ( 8) hydrogen bonds : bond 0.06595 / 4.46 ( 1404) hydrogen bonds : angle 3.42847 / 2.46 ( 4104) metal coordination : bond 0.00437 / 0.35 ( 16) metal coordination : angle 1.55925 / 1.01 ( 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 357 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 257 time to evaluate : 0.854 Fit side-chains REVERT: A 186 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: A 383 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7312 (mp) REVERT: A 422 MET cc_start: 0.6572 (tmm) cc_final: 0.6296 (tmt) REVERT: A 521 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7765 (mp) REVERT: A 551 ASN cc_start: 0.7875 (t0) cc_final: 0.7501 (t0) REVERT: C 272 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7595 (ttt180) REVERT: C 335 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7262 (mpp) REVERT: C 391 THR cc_start: 0.3673 (OUTLIER) cc_final: 0.3455 (p) REVERT: C 422 MET cc_start: 0.6594 (tmm) cc_final: 0.6261 (ttt) REVERT: C 520 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: C 521 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7716 (mp) REVERT: B 160 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8312 (tp) REVERT: B 335 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7285 (mpp) REVERT: B 383 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7262 (mp) REVERT: B 422 MET cc_start: 0.6580 (tmm) cc_final: 0.6255 (ttt) REVERT: B 521 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7762 (mp) REVERT: B 551 ASN cc_start: 0.7874 (t0) cc_final: 0.7500 (t0) REVERT: D 160 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8292 (tp) REVERT: D 335 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7290 (mpp) REVERT: D 422 MET cc_start: 0.6578 (tmm) cc_final: 0.6258 (ttt) REVERT: D 521 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7775 (mp) REVERT: D 551 ASN cc_start: 0.7880 (t0) cc_final: 0.7503 (t0) outliers start: 100 outliers final: 67 residues processed: 327 average time/residue: 0.5405 time to fit residues: 204.8812 Evaluate side-chains 335 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 253 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 184 SER Chi-restraints excluded: chain A residue 186 GLU 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 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 407 ILE 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 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 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 253 LYS 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 391 THR Chi-restraints excluded: chain C residue 407 ILE 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 710 ASN Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 184 SER 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 253 LYS 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 343 MET 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 710 ASN Chi-restraints excluded: chain D residue 61 VAL 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 343 MET 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 710 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 191 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN C 154 ASN C 386 GLN C 551 ASN B 386 GLN D 386 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.183751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126635 restraints weight = 24038.411| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.15 r_work: 0.3395 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22784 Z= 0.155 Angle : 0.574 9.476 30840 Z= 0.290 Chirality : 0.039 0.242 3468 Planarity : 0.004 0.043 3808 Dihedral : 11.143 147.102 3598 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.51 % Allowed : 20.36 % Favored : 76.13 % 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: 2.11 (0.16), residues: 2668 helix: 2.31 (0.12), residues: 1956 sheet: None (None), residues: 0 loop : -1.30 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 71 TYR 0.018 0.001 TYR A 524 PHE 0.015 0.002 PHE B 341 TRP 0.014 0.001 TRP A 315 HIS 0.002 0.001 HIS C 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (22764) covalent geometry : angle 0.57324 / 0.29 (30820) SS BOND : bond 0.00338 / 0.17 ( 4) SS BOND : angle 0.86198 / 0.54 ( 8) hydrogen bonds : bond 0.06406 / 4.33 ( 1404) hydrogen bonds : angle 3.42578 / 2.45 ( 4104) metal coordination : bond 0.00454 / 0.36 ( 16) metal coordination : angle 1.51117 / 0.99 ( 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 333 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 252 time to evaluate : 0.831 Fit side-chains REVERT: A 383 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7204 (mp) REVERT: A 422 MET cc_start: 0.6519 (tmm) cc_final: 0.6234 (ttt) REVERT: A 521 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7651 (mp) REVERT: A 551 ASN cc_start: 0.7854 (t0) cc_final: 0.7463 (t0) REVERT: C 272 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7533 (ttt180) REVERT: C 335 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7233 (mpp) REVERT: C 391 THR cc_start: 0.3706 (OUTLIER) cc_final: 0.3483 (p) REVERT: C 422 MET cc_start: 0.6638 (tmm) cc_final: 0.6286 (ttt) REVERT: C 521 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7669 (mp) REVERT: B 160 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8265 (tp) REVERT: B 335 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7255 (mpp) REVERT: B 383 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7235 (mp) REVERT: B 422 MET cc_start: 0.6640 (tmm) cc_final: 0.6288 (ttt) REVERT: B 521 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7637 (mp) REVERT: B 551 ASN cc_start: 0.7847 (t0) cc_final: 0.7466 (t0) REVERT: D 160 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8256 (tp) REVERT: D 335 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7243 (mpp) REVERT: D 422 MET cc_start: 0.6654 (tmm) cc_final: 0.6301 (ttt) REVERT: D 521 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7653 (mp) REVERT: D 551 ASN cc_start: 0.7833 (t0) cc_final: 0.7453 (t0) outliers start: 81 outliers final: 56 residues processed: 309 average time/residue: 0.5843 time to fit residues: 208.3159 Evaluate side-chains 314 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 245 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 184 SER 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 253 LYS Chi-restraints excluded: chain A residue 304 GLN 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 710 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 211 LEU 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 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 391 THR 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 710 ASN Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 184 SER 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 253 LYS 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 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 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 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 518 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 544 THR 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: 8.9990 chunk 149 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN C 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.183315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125488 restraints weight = 23885.002| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.98 r_work: 0.3411 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22784 Z= 0.162 Angle : 0.588 10.271 30840 Z= 0.295 Chirality : 0.039 0.274 3468 Planarity : 0.004 0.044 3808 Dihedral : 11.169 146.232 3598 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.51 % Allowed : 20.41 % Favored : 76.08 % 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: 2.06 (0.16), residues: 2668 helix: 2.27 (0.12), residues: 1956 sheet: None (None), residues: 0 loop : -1.30 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 71 TYR 0.017 0.001 TYR C 524 PHE 0.015 0.002 PHE C 341 TRP 0.015 0.001 TRP D 315 HIS 0.003 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (22764) covalent geometry : angle 0.58719 / 0.30 (30820) SS BOND : bond 0.00374 / 0.19 ( 4) SS BOND : angle 0.92493 / 0.58 ( 8) hydrogen bonds : bond 0.06627 / 4.47 ( 1404) hydrogen bonds : angle 3.46141 / 2.48 ( 4104) metal coordination : bond 0.00519 / 0.42 ( 16) metal coordination : angle 1.59714 / 1.06 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9076.58 seconds wall clock time: 154 minutes 44.86 seconds (9284.86 seconds total)