Starting phenix.real_space_refine on Sat Jul 4 02:57:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8slx_40582/07_2026/8slx_40582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slx_40582/07_2026/8slx_40582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8slx_40582/07_2026/8slx_40582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slx_40582/07_2026/8slx_40582.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8slx_40582/07_2026/8slx_40582.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8slx_40582/07_2026/8slx_40582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8slx_40582/07_2026/8slx_40582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slx_40582/07_2026/8slx_40582.map" } resolution = 3.23 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= 0.002 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 Na 1 4.78 5 C 11800 2.51 5 N 3012 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 17885 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4447 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 18, 'TRANS': 575} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 528 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 12, 'ARG:plan': 12, 'GLU:plan': 20, 'TYR:plan': 3, 'TRP:plan': 2, 'GLN:plan1': 6, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 271 Chain: "B" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4447 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 18, 'TRANS': 575} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 528 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 12, 'ARG:plan': 12, 'GLU:plan': 20, 'TYR:plan': 3, 'TRP:plan': 2, 'GLN:plan1': 6, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 271 Chain: "C" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4447 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 18, 'TRANS': 575} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 528 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 12, 'ARG:plan': 12, 'GLU:plan': 20, 'TYR:plan': 3, 'TRP:plan': 2, 'GLN:plan1': 6, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 271 Chain: "D" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4447 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 18, 'TRANS': 575} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 528 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 12, 'ARG:plan': 12, 'GLU:plan': 20, 'TYR:plan': 3, 'TRP:plan': 2, 'GLN:plan1': 6, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 271 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' NA': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.95, per 1000 atoms: 0.22 Number of scatterers: 17885 At special positions: 0 Unit cell: (155.21, 155.21, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 Na 1 11.00 O 2976 8.00 N 3012 7.00 C 11800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.55 Conformation dependent library (CDL) restraints added in 703.5 milliseconds 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 65.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.533A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.911A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 102 removed outlier: 4.363A pdb=" N ARG A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.763A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.699A pdb=" N HIS A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 413 Processing helix chain 'A' and resid 433 through 459 Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.813A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.925A pdb=" N ILE A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 removed outlier: 4.096A pdb=" N GLN A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 560 removed outlier: 4.010A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 650 removed outlier: 3.567A pdb=" N LEU A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.534A pdb=" N ARG B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.912A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 102 removed outlier: 4.362A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.762A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 366 through 370 removed outlier: 4.698A pdb=" N HIS B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 413 Processing helix chain 'B' and resid 433 through 459 Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.813A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.925A pdb=" N ILE B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 removed outlier: 4.096A pdb=" N GLN B 530 " --> pdb=" O SER B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 560 removed outlier: 4.011A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 650 removed outlier: 3.566A pdb=" N LEU B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER B 656 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.533A pdb=" N ARG C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.912A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 102 removed outlier: 4.363A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP C 145 " --> pdb=" O GLN C 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.763A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 366 through 370 removed outlier: 4.699A pdb=" N HIS C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 413 Processing helix chain 'C' and resid 433 through 459 Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.812A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.924A pdb=" N ILE C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 531 removed outlier: 4.097A pdb=" N GLN C 530 " --> pdb=" O SER C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 560 removed outlier: 4.010A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 650 removed outlier: 3.566A pdb=" N LEU C 623 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.533A pdb=" N ARG D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.911A pdb=" N LEU D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 102 removed outlier: 4.363A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP D 145 " --> pdb=" O GLN D 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.763A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 366 through 370 removed outlier: 4.698A pdb=" N HIS D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 413 Processing helix chain 'D' and resid 433 through 459 Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.813A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 526 removed outlier: 3.925A pdb=" N ILE D 524 " --> pdb=" O GLN D 520 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 531 removed outlier: 4.097A pdb=" N GLN D 530 " --> pdb=" O SER D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 560 removed outlier: 4.010A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 650 removed outlier: 3.567A pdb=" N LEU D 623 " --> pdb=" O ARG D 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER D 656 " --> pdb=" O VAL D 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 689 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 689 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 689 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 689 " --> pdb=" O ARG D 702 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 3012 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: 3.45 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5568 1.34 - 1.46: 4551 1.46 - 1.58: 8045 1.58 - 1.69: 12 1.69 - 1.81: 140 Bond restraints: 18316 Sorted by residual: bond pdb=" C05 P0T D 802 " pdb=" C06 P0T D 802 " ideal model delta sigma weight residual 1.521 1.660 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C05 P0T A 801 " pdb=" C06 P0T A 801 " ideal model delta sigma weight residual 1.521 1.660 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C05 P0T D 801 " pdb=" C06 P0T D 801 " ideal model delta sigma weight residual 1.521 1.659 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C05 P0T C 801 " pdb=" C06 P0T C 801 " ideal model delta sigma weight residual 1.521 1.659 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C03 P0T C 801 " pdb=" C04 P0T C 801 " ideal model delta sigma weight residual 1.548 1.675 -0.127 2.00e-02 2.50e+03 4.05e+01 ... (remaining 18311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 24648 1.62 - 3.24: 248 3.24 - 4.86: 80 4.86 - 6.49: 12 6.49 - 8.11: 8 Bond angle restraints: 24996 Sorted by residual: angle pdb=" C04 P0T A 801 " pdb=" C07 P0T A 801 " pdb=" C09 P0T A 801 " ideal model delta sigma weight residual 125.00 116.89 8.11 3.00e+00 1.11e-01 7.30e+00 angle pdb=" C04 P0T D 802 " pdb=" C07 P0T D 802 " pdb=" C09 P0T D 802 " ideal model delta sigma weight residual 125.00 116.90 8.10 3.00e+00 1.11e-01 7.30e+00 angle pdb=" C04 P0T C 801 " pdb=" C07 P0T C 801 " pdb=" C09 P0T C 801 " ideal model delta sigma weight residual 125.00 116.92 8.08 3.00e+00 1.11e-01 7.26e+00 angle pdb=" C04 P0T D 801 " pdb=" C07 P0T D 801 " pdb=" C09 P0T D 801 " ideal model delta sigma weight residual 125.00 116.93 8.07 3.00e+00 1.11e-01 7.24e+00 angle pdb=" N VAL B 190 " pdb=" CA VAL B 190 " pdb=" C VAL B 190 " ideal model delta sigma weight residual 112.29 109.81 2.48 9.40e-01 1.13e+00 6.96e+00 ... (remaining 24991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.84: 10196 27.84 - 55.67: 320 55.67 - 83.51: 24 83.51 - 111.34: 0 111.34 - 139.18: 4 Dihedral angle restraints: 10544 sinusoidal: 3600 harmonic: 6944 Sorted by residual: dihedral pdb=" C20 P0T D 802 " pdb=" C21 P0T D 802 " pdb=" C22 P0T D 802 " pdb=" C23 P0T D 802 " ideal model delta sinusoidal sigma weight residual 180.45 41.27 139.18 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" C20 P0T A 801 " pdb=" C21 P0T A 801 " pdb=" C22 P0T A 801 " pdb=" C23 P0T A 801 " ideal model delta sinusoidal sigma weight residual 180.45 41.34 139.11 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" C20 P0T D 801 " pdb=" C21 P0T D 801 " pdb=" C22 P0T D 801 " pdb=" C23 P0T D 801 " ideal model delta sinusoidal sigma weight residual 180.45 41.36 139.09 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 10541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2948 0.123 - 0.247: 0 0.247 - 0.370: 0 0.370 - 0.494: 0 0.494 - 0.617: 4 Chirality restraints: 2952 Sorted by residual: chirality pdb=" C03 P0T A 801 " pdb=" C04 P0T A 801 " pdb=" C05 P0T A 801 " pdb=" C10 P0T A 801 " both_signs ideal model delta sigma weight residual False -2.55 -3.17 0.62 2.00e-01 2.50e+01 9.52e+00 chirality pdb=" C03 P0T C 801 " pdb=" C04 P0T C 801 " pdb=" C05 P0T C 801 " pdb=" C10 P0T C 801 " both_signs ideal model delta sigma weight residual False -2.55 -3.16 0.62 2.00e-01 2.50e+01 9.52e+00 chirality pdb=" C03 P0T D 801 " pdb=" C04 P0T D 801 " pdb=" C05 P0T D 801 " pdb=" C10 P0T D 801 " both_signs ideal model delta sigma weight residual False -2.55 -3.16 0.62 2.00e-01 2.50e+01 9.49e+00 ... (remaining 2949 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 321 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO B 322 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 322 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 322 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 321 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 322 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 321 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO C 322 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " -0.017 5.00e-02 4.00e+02 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 6349 2.86 - 3.37: 17501 3.37 - 3.88: 29391 3.88 - 4.39: 33171 4.39 - 4.90: 56054 Nonbonded interactions: 142466 Sorted by model distance: nonbonded pdb=" O LEU D 216 " pdb=" OG1 THR D 220 " model vdw 2.353 3.040 nonbonded pdb=" O LEU B 216 " pdb=" OG1 THR B 220 " model vdw 2.353 3.040 nonbonded pdb=" O LEU A 216 " pdb=" OG1 THR A 220 " model vdw 2.354 3.040 nonbonded pdb=" O LEU C 216 " pdb=" OG1 THR C 220 " model vdw 2.354 3.040 nonbonded pdb=" O TRP D 457 " pdb=" NH2 ARG D 460 " model vdw 2.357 3.120 ... (remaining 142461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 75 through 728) selection = chain 'B' selection = (chain 'C' and resid 75 through 728) selection = (chain 'D' and resid 75 through 728) } 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.290 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.004 0.139 18316 Z= 0.200 Angle : 0.479 8.107 24996 Z= 0.228 Chirality : 0.041 0.617 2952 Planarity : 0.002 0.030 3068 Dihedral : 13.366 139.178 6040 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 1.44 (0.17), residues: 2328 helix: 1.79 (0.14), residues: 1312 sheet: 0.62 (0.55), residues: 88 loop : -0.15 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 560 TYR 0.015 0.001 TYR D 162 PHE 0.011 0.001 PHE D 547 TRP 0.005 0.001 TRP A 496 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 (18316) covalent geometry : angle 0.47869 / 0.23 (24996) hydrogen bonds : bond 0.25001 / 16.79 ( 1040) hydrogen bonds : angle 6.39841 / 4.63 ( 3012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.605 Fit side-chains REVERT: C 158 THR cc_start: 0.8977 (m) cc_final: 0.8754 (t) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.0937 time to fit residues: 36.2924 Evaluate side-chains 185 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 487 GLN A 639 ASN B 294 GLN B 487 GLN B 639 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 GLN C 438 HIS C 487 GLN C 639 ASN D 294 GLN D 487 GLN D 639 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.109156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.093714 restraints weight = 43115.766| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.90 r_work: 0.3426 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18316 Z= 0.104 Angle : 0.474 6.792 24996 Z= 0.237 Chirality : 0.036 0.144 2952 Planarity : 0.003 0.030 3068 Dihedral : 6.116 96.996 2552 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.84 % Allowed : 6.41 % Favored : 92.75 % 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: 1.94 (0.17), residues: 2328 helix: 2.16 (0.14), residues: 1392 sheet: 0.67 (0.56), residues: 88 loop : -0.08 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 702 TYR 0.012 0.001 TYR A 162 PHE 0.012 0.001 PHE D 407 TRP 0.007 0.001 TRP B 509 HIS 0.003 0.000 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (18316) covalent geometry : angle 0.47432 / 0.24 (24996) hydrogen bonds : bond 0.03841 / 2.57 ( 1040) hydrogen bonds : angle 4.04131 / 2.93 ( 3012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.584 Fit side-chains REVERT: A 272 ASP cc_start: 0.8002 (p0) cc_final: 0.7774 (p0) outliers start: 14 outliers final: 10 residues processed: 202 average time/residue: 0.0944 time to fit residues: 32.1374 Evaluate side-chains 184 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 630 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 107 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.105827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.090216 restraints weight = 43555.725| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.91 r_work: 0.3365 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18316 Z= 0.145 Angle : 0.498 7.804 24996 Z= 0.248 Chirality : 0.037 0.141 2952 Planarity : 0.003 0.033 3068 Dihedral : 4.459 63.710 2552 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.26 % Allowed : 10.01 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.18), residues: 2328 helix: 2.38 (0.14), residues: 1372 sheet: 0.54 (0.56), residues: 88 loop : 0.03 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.011 0.001 TYR A 162 PHE 0.019 0.001 PHE C 601 TRP 0.008 0.001 TRP C 496 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (18316) covalent geometry : angle 0.49766 / 0.25 (24996) hydrogen bonds : bond 0.03683 / 2.48 ( 1040) hydrogen bonds : angle 3.88374 / 2.81 ( 3012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.733 Fit side-chains REVERT: A 634 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: B 496 TRP cc_start: 0.8541 (OUTLIER) cc_final: 0.8114 (t-100) REVERT: B 634 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: C 634 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: D 634 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.8103 (m-80) outliers start: 21 outliers final: 13 residues processed: 189 average time/residue: 0.0990 time to fit residues: 31.7257 Evaluate side-chains 182 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 496 TRP Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 208 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.105731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.090227 restraints weight = 43468.099| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.90 r_work: 0.3363 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18316 Z= 0.135 Angle : 0.479 8.092 24996 Z= 0.237 Chirality : 0.036 0.139 2952 Planarity : 0.003 0.034 3068 Dihedral : 3.855 51.444 2552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.98 % Allowed : 11.99 % Favored : 86.03 % 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 (0.18), residues: 2328 helix: 2.46 (0.14), residues: 1372 sheet: 0.41 (0.54), residues: 88 loop : 0.07 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 369 TYR 0.010 0.001 TYR B 228 PHE 0.015 0.001 PHE B 601 TRP 0.006 0.001 TRP A 333 HIS 0.003 0.001 HIS D 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (18316) covalent geometry : angle 0.47862 / 0.24 (24996) hydrogen bonds : bond 0.03340 / 2.24 ( 1040) hydrogen bonds : angle 3.79027 / 2.74 ( 3012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.646 Fit side-chains REVERT: A 634 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: B 634 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: C 634 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: D 634 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7841 (m-80) outliers start: 33 outliers final: 24 residues processed: 183 average time/residue: 0.0944 time to fit residues: 29.5925 Evaluate side-chains 192 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 496 TRP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 496 TRP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 167 optimal weight: 0.7980 chunk 231 optimal weight: 0.9990 chunk 142 optimal weight: 0.0470 chunk 152 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.107919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092490 restraints weight = 43171.177| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.91 r_work: 0.3408 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18316 Z= 0.090 Angle : 0.448 8.056 24996 Z= 0.218 Chirality : 0.035 0.137 2952 Planarity : 0.002 0.033 3068 Dihedral : 3.550 43.359 2552 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.22 % Allowed : 12.89 % Favored : 84.89 % 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: 2.38 (0.18), residues: 2328 helix: 2.60 (0.14), residues: 1368 sheet: 0.54 (0.52), residues: 88 loop : 0.06 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 702 TYR 0.008 0.001 TYR A 162 PHE 0.009 0.001 PHE C 407 TRP 0.006 0.001 TRP A 333 HIS 0.001 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (18316) covalent geometry : angle 0.44783 / 0.22 (24996) hydrogen bonds : bond 0.02973 / 1.99 ( 1040) hydrogen bonds : angle 3.57666 / 2.59 ( 3012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.651 Fit side-chains REVERT: A 272 ASP cc_start: 0.8024 (p0) cc_final: 0.7784 (p0) REVERT: A 634 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: B 634 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: C 634 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: D 634 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7802 (m-80) outliers start: 37 outliers final: 29 residues processed: 207 average time/residue: 0.0974 time to fit residues: 34.0580 Evaluate side-chains 210 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 496 TRP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 187 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 438 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.105672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.090100 restraints weight = 42750.419| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.88 r_work: 0.3363 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18316 Z= 0.139 Angle : 0.484 7.510 24996 Z= 0.237 Chirality : 0.036 0.146 2952 Planarity : 0.003 0.035 3068 Dihedral : 3.676 44.959 2552 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.40 % Allowed : 13.07 % Favored : 84.53 % 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: 2.38 (0.18), residues: 2328 helix: 2.56 (0.14), residues: 1372 sheet: 0.41 (0.52), residues: 88 loop : 0.14 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 560 TYR 0.009 0.001 TYR B 228 PHE 0.021 0.001 PHE B 407 TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (18316) covalent geometry : angle 0.48364 / 0.24 (24996) hydrogen bonds : bond 0.03285 / 2.20 ( 1040) hydrogen bonds : angle 3.65921 / 2.65 ( 3012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.564 Fit side-chains REVERT: A 634 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: B 634 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: C 634 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: D 634 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7789 (m-80) outliers start: 40 outliers final: 33 residues processed: 198 average time/residue: 0.0935 time to fit residues: 31.5416 Evaluate side-chains 209 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 201 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 0.0030 chunk 52 optimal weight: 8.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 HIS B 234 HIS C 413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.104453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.088834 restraints weight = 43232.139| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.91 r_work: 0.3340 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18316 Z= 0.161 Angle : 0.507 7.892 24996 Z= 0.248 Chirality : 0.036 0.162 2952 Planarity : 0.003 0.034 3068 Dihedral : 3.783 45.219 2552 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.18 % Allowed : 13.37 % Favored : 83.45 % 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: 2.32 (0.18), residues: 2328 helix: 2.49 (0.14), residues: 1372 sheet: 0.25 (0.53), residues: 88 loop : 0.18 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 560 TYR 0.010 0.001 TYR B 228 PHE 0.016 0.001 PHE D 407 TRP 0.006 0.001 TRP C 333 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (18316) covalent geometry : angle 0.50665 / 0.25 (24996) hydrogen bonds : bond 0.03411 / 2.29 ( 1040) hydrogen bonds : angle 3.70759 / 2.68 ( 3012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 167 time to evaluate : 0.582 Fit side-chains REVERT: A 634 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: B 548 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6833 (tp) REVERT: B 634 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: C 634 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: D 634 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7774 (m-80) outliers start: 53 outliers final: 34 residues processed: 200 average time/residue: 0.0977 time to fit residues: 33.3699 Evaluate side-chains 200 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 172 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 119 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 200 optimal weight: 0.1980 chunk 136 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.108192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.092861 restraints weight = 42424.333| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.88 r_work: 0.3411 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18316 Z= 0.084 Angle : 0.448 7.885 24996 Z= 0.217 Chirality : 0.035 0.143 2952 Planarity : 0.003 0.034 3068 Dihedral : 3.428 36.239 2552 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.52 % Allowed : 14.09 % Favored : 83.39 % 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: 2.44 (0.18), residues: 2328 helix: 2.61 (0.14), residues: 1368 sheet: 0.33 (0.52), residues: 88 loop : 0.18 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 684 TYR 0.009 0.001 TYR C 228 PHE 0.014 0.001 PHE B 407 TRP 0.007 0.001 TRP A 333 HIS 0.001 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.08 (18316) covalent geometry : angle 0.44786 / 0.22 (24996) hydrogen bonds : bond 0.02894 / 1.93 ( 1040) hydrogen bonds : angle 3.51571 / 2.54 ( 3012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.594 Fit side-chains REVERT: A 634 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: B 634 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: C 634 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: D 548 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6789 (tp) REVERT: D 634 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7780 (m-80) outliers start: 42 outliers final: 31 residues processed: 202 average time/residue: 0.0866 time to fit residues: 29.9842 Evaluate side-chains 204 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 496 TRP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 234 optimal weight: 8.9990 chunk 137 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.107393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.091896 restraints weight = 42581.148| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.91 r_work: 0.3392 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18316 Z= 0.098 Angle : 0.466 9.016 24996 Z= 0.224 Chirality : 0.035 0.161 2952 Planarity : 0.003 0.035 3068 Dihedral : 3.453 37.830 2552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.00 % Allowed : 13.25 % Favored : 83.75 % 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: 2.48 (0.18), residues: 2328 helix: 2.63 (0.14), residues: 1372 sheet: 0.39 (0.52), residues: 88 loop : 0.21 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 560 TYR 0.008 0.001 TYR D 228 PHE 0.014 0.001 PHE B 407 TRP 0.006 0.001 TRP C 333 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (18316) covalent geometry : angle 0.46626 / 0.22 (24996) hydrogen bonds : bond 0.03006 / 2.01 ( 1040) hydrogen bonds : angle 3.51688 / 2.54 ( 3012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.563 Fit side-chains REVERT: A 548 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6874 (tp) REVERT: A 634 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: B 634 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: B 640 MET cc_start: 0.8423 (ppp) cc_final: 0.7885 (tpt) REVERT: C 634 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: D 548 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6901 (tp) REVERT: D 634 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7770 (m-80) outliers start: 50 outliers final: 39 residues processed: 206 average time/residue: 0.0950 time to fit residues: 33.5436 Evaluate side-chains 214 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 689 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 93 optimal weight: 0.9990 chunk 206 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 219 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.107989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092458 restraints weight = 42605.189| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.92 r_work: 0.3406 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18316 Z= 0.093 Angle : 0.462 9.025 24996 Z= 0.222 Chirality : 0.035 0.157 2952 Planarity : 0.003 0.035 3068 Dihedral : 3.411 37.297 2552 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.64 % Allowed : 13.85 % Favored : 83.51 % 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: 2.53 (0.18), residues: 2328 helix: 2.66 (0.14), residues: 1372 sheet: 0.45 (0.52), residues: 88 loop : 0.23 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 560 TYR 0.008 0.001 TYR A 228 PHE 0.013 0.001 PHE B 407 TRP 0.006 0.001 TRP C 333 HIS 0.001 0.000 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (18316) covalent geometry : angle 0.46212 / 0.22 (24996) hydrogen bonds : bond 0.02936 / 1.97 ( 1040) hydrogen bonds : angle 3.48400 / 2.51 ( 3012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.742 Fit side-chains REVERT: A 272 ASP cc_start: 0.8010 (p0) cc_final: 0.7738 (p0) REVERT: A 548 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6880 (tp) REVERT: A 634 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: B 272 ASP cc_start: 0.8022 (p0) cc_final: 0.7747 (p0) REVERT: B 634 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: B 640 MET cc_start: 0.8371 (ppp) cc_final: 0.8035 (tpp) REVERT: C 272 ASP cc_start: 0.8033 (p0) cc_final: 0.7761 (p0) REVERT: C 634 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: D 272 ASP cc_start: 0.8068 (p0) cc_final: 0.7791 (p0) REVERT: D 548 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6837 (tp) REVERT: D 634 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7769 (m-80) outliers start: 44 outliers final: 37 residues processed: 210 average time/residue: 0.0913 time to fit residues: 32.6986 Evaluate side-chains 215 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 689 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 15 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 220 optimal weight: 0.0980 chunk 89 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 GLN B 294 GLN C 294 GLN D 294 GLN D 639 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.109654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094123 restraints weight = 42536.720| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.94 r_work: 0.3431 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18316 Z= 0.080 Angle : 0.448 8.916 24996 Z= 0.214 Chirality : 0.035 0.164 2952 Planarity : 0.002 0.035 3068 Dihedral : 3.296 33.688 2552 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.58 % Allowed : 14.33 % Favored : 83.09 % 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: 2.55 (0.18), residues: 2328 helix: 2.71 (0.14), residues: 1368 sheet: 0.54 (0.52), residues: 88 loop : 0.18 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 560 TYR 0.008 0.001 TYR C 228 PHE 0.013 0.001 PHE D 407 TRP 0.007 0.001 TRP C 333 HIS 0.001 0.000 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.08 (18316) covalent geometry : angle 0.44781 / 0.21 (24996) hydrogen bonds : bond 0.02741 / 1.84 ( 1040) hydrogen bonds : angle 3.40690 / 2.46 ( 3012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3614.52 seconds wall clock time: 62 minutes 50.42 seconds (3770.42 seconds total)