Starting phenix.real_space_refine on Sun Jun 15 22:55:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slx_40582/06_2025/8slx_40582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slx_40582/06_2025/8slx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8slx_40582/06_2025/8slx_40582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slx_40582/06_2025/8slx_40582.map" model { file = "/net/cci-nas-00/data/ceres_data/8slx_40582/06_2025/8slx_40582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slx_40582/06_2025/8slx_40582.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17885 Number of models: 1 Model: "" Number of chains: 7 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: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 12} 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} Restraints were copied for chains: B, C, D Time building chain proxies: 10.52, per 1000 atoms: 0.59 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: 4.66 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.67 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: 5.40 Time building geometry restraints manager: 5.13 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: 10252 27.84 - 55.67: 328 55.67 - 83.51: 24 83.51 - 111.34: 0 111.34 - 139.18: 4 Dihedral angle restraints: 10608 sinusoidal: 3664 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 10605 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: 2.110 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 39.610 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 13.461 139.178 6104 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP A 496 HIS 0.002 0.000 HIS B 165 PHE 0.011 0.001 PHE D 547 TYR 0.015 0.001 TYR D 162 ARG 0.001 0.000 ARG D 560 Details of bonding type rmsd hydrogen bonds : bond 0.25001 ( 1040) hydrogen bonds : angle 6.39841 ( 3012) covalent geometry : bond 0.00400 (18316) covalent geometry : angle 0.47869 (24996) *********************** 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 : 1.984 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: 0.2370 time to fit residues: 91.1842 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 : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.9990 chunk 178 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.105091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089297 restraints weight = 43044.997| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.92 r_work: 0.3344 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18316 Z= 0.189 Angle : 0.553 7.619 24996 Z= 0.275 Chirality : 0.038 0.138 2952 Planarity : 0.003 0.033 3068 Dihedral : 6.307 96.228 2616 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.20 % Allowed : 7.67 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.18), residues: 2328 helix: 1.96 (0.14), residues: 1396 sheet: 0.67 (0.58), residues: 88 loop : -0.10 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 496 HIS 0.005 0.001 HIS B 169 PHE 0.014 0.001 PHE B 407 TYR 0.013 0.002 TYR A 162 ARG 0.003 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 1040) hydrogen bonds : angle 4.16299 ( 3012) covalent geometry : bond 0.00444 (18316) covalent geometry : angle 0.55268 (24996) *********************** 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 202 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.994 Fit side-chains REVERT: A 634 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: B 634 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: C 634 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: D 634 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.8072 (m-80) outliers start: 20 outliers final: 14 residues processed: 190 average time/residue: 0.2258 time to fit residues: 72.4727 Evaluate side-chains 177 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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 630 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 545 LEU 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 441 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 137 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.107889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092384 restraints weight = 42764.319| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.93 r_work: 0.3402 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2117 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= 0.096 Angle : 0.457 7.019 24996 Z= 0.227 Chirality : 0.035 0.124 2952 Planarity : 0.003 0.032 3068 Dihedral : 4.765 67.786 2616 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.08 % Allowed : 10.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.18), residues: 2328 helix: 2.38 (0.14), residues: 1372 sheet: 0.51 (0.56), residues: 88 loop : 0.00 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 333 HIS 0.002 0.000 HIS A 165 PHE 0.008 0.001 PHE B 407 TYR 0.010 0.001 TYR A 162 ARG 0.001 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 1040) hydrogen bonds : angle 3.79069 ( 3012) covalent geometry : bond 0.00211 (18316) covalent geometry : angle 0.45664 (24996) *********************** 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: 18 poor density : 182 time to evaluate : 2.161 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 191 average time/residue: 0.2360 time to fit residues: 76.4059 Evaluate side-chains 183 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 630 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 42 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.108683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093136 restraints weight = 43045.279| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.92 r_work: 0.3416 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18316 Z= 0.088 Angle : 0.439 7.150 24996 Z= 0.218 Chirality : 0.035 0.127 2952 Planarity : 0.003 0.032 3068 Dihedral : 3.964 53.119 2616 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.44 % Allowed : 11.45 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.18), residues: 2328 helix: 2.55 (0.14), residues: 1372 sheet: 0.48 (0.54), residues: 88 loop : 0.03 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 333 HIS 0.001 0.000 HIS B 251 PHE 0.020 0.001 PHE B 407 TYR 0.009 0.001 TYR A 162 ARG 0.001 0.000 ARG D 560 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 1040) hydrogen bonds : angle 3.60369 ( 3012) covalent geometry : bond 0.00195 (18316) covalent geometry : angle 0.43908 (24996) *********************** 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 208 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 2.136 Fit side-chains REVERT: A 634 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: B 634 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: C 634 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: D 634 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7975 (m-80) outliers start: 24 outliers final: 15 residues processed: 196 average time/residue: 0.2330 time to fit residues: 78.5656 Evaluate side-chains 196 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 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 436 LEU 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 496 TRP 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 152 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 496 TRP 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 100 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.104741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.089045 restraints weight = 43407.626| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.95 r_work: 0.3342 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18316 Z= 0.164 Angle : 0.514 9.228 24996 Z= 0.251 Chirality : 0.036 0.144 2952 Planarity : 0.003 0.034 3068 Dihedral : 4.229 51.255 2616 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.52 % Allowed : 11.87 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.18), residues: 2328 helix: 2.50 (0.14), residues: 1372 sheet: 0.25 (0.53), residues: 88 loop : 0.10 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 715 HIS 0.003 0.001 HIS C 165 PHE 0.014 0.001 PHE B 407 TYR 0.010 0.001 TYR B 228 ARG 0.002 0.000 ARG D 560 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 1040) hydrogen bonds : angle 3.75093 ( 3012) covalent geometry : bond 0.00386 (18316) covalent geometry : angle 0.51391 (24996) *********************** 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 205 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 2.205 Fit side-chains REVERT: A 634 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: B 634 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: C 634 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: D 634 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7835 (m-80) outliers start: 42 outliers final: 30 residues processed: 186 average time/residue: 0.2350 time to fit residues: 75.8167 Evaluate side-chains 189 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 545 LEU 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 152 LEU 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 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 502 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 235 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 162 optimal weight: 0.0370 chunk 82 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 233 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.108188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092552 restraints weight = 42933.012| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.96 r_work: 0.3404 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2566 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 : 0.435 7.197 24996 Z= 0.213 Chirality : 0.035 0.127 2952 Planarity : 0.002 0.033 3068 Dihedral : 3.723 37.152 2616 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.92 % Allowed : 13.79 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.18), residues: 2328 helix: 2.52 (0.14), residues: 1392 sheet: 0.39 (0.52), residues: 88 loop : 0.17 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.001 0.000 HIS C 165 PHE 0.011 0.001 PHE B 407 TYR 0.008 0.001 TYR A 162 ARG 0.001 0.000 ARG D 560 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 1040) hydrogen bonds : angle 3.51055 ( 3012) covalent geometry : bond 0.00185 (18316) covalent geometry : angle 0.43486 (24996) *********************** 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 209 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 2.132 Fit side-chains REVERT: A 272 ASP cc_start: 0.8009 (p0) cc_final: 0.7775 (p0) REVERT: A 634 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: B 634 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: C 634 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: D 634 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7785 (m-80) outliers start: 32 outliers final: 27 residues processed: 189 average time/residue: 0.2362 time to fit residues: 75.7450 Evaluate side-chains 204 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 545 LEU Chi-restraints excluded: chain A residue 546 VAL 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 545 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 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 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 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 496 TRP Chi-restraints excluded: chain D residue 502 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 168 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 67 optimal weight: 0.0770 chunk 21 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.107282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091662 restraints weight = 42902.505| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.96 r_work: 0.3386 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2616 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= 0.099 Angle : 0.454 8.726 24996 Z= 0.219 Chirality : 0.035 0.144 2952 Planarity : 0.002 0.033 3068 Dihedral : 3.757 37.709 2616 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.46 % Allowed : 13.67 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.18), residues: 2328 helix: 2.56 (0.14), residues: 1396 sheet: 0.38 (0.52), residues: 88 loop : 0.24 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.002 0.000 HIS C 165 PHE 0.010 0.001 PHE B 407 TYR 0.008 0.001 TYR C 228 ARG 0.001 0.000 ARG A 560 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 1040) hydrogen bonds : angle 3.52307 ( 3012) covalent geometry : bond 0.00228 (18316) covalent geometry : angle 0.45379 (24996) *********************** 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 209 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 2.137 Fit side-chains REVERT: A 272 ASP cc_start: 0.8008 (p0) cc_final: 0.7748 (p0) REVERT: A 634 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: B 634 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: C 634 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: D 634 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7747 (m-80) outliers start: 41 outliers final: 32 residues processed: 189 average time/residue: 0.2306 time to fit residues: 74.0042 Evaluate side-chains 201 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 234 HIS 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 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 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 502 VAL 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 158 THR Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 502 VAL 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 77 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 chunk 118 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.105641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.089969 restraints weight = 42860.935| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.92 r_work: 0.3358 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2637 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= 0.136 Angle : 0.489 9.022 24996 Z= 0.237 Chirality : 0.036 0.170 2952 Planarity : 0.003 0.033 3068 Dihedral : 3.941 40.028 2616 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.52 % Allowed : 13.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.18), residues: 2328 helix: 2.48 (0.14), residues: 1396 sheet: 0.22 (0.52), residues: 88 loop : 0.26 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 509 HIS 0.003 0.001 HIS B 165 PHE 0.012 0.001 PHE B 601 TYR 0.009 0.001 TYR D 162 ARG 0.002 0.000 ARG A 560 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 1040) hydrogen bonds : angle 3.61817 ( 3012) covalent geometry : bond 0.00323 (18316) covalent geometry : angle 0.48898 (24996) *********************** 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 205 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 1.951 Fit side-chains REVERT: A 634 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: A 640 MET cc_start: 0.8629 (tmm) cc_final: 0.8089 (tpt) REVERT: B 548 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6835 (tp) REVERT: B 634 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: C 634 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: D 634 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: D 640 MET cc_start: 0.8633 (tmm) cc_final: 0.8121 (tpt) outliers start: 42 outliers final: 32 residues processed: 186 average time/residue: 0.2323 time to fit residues: 74.3520 Evaluate side-chains 199 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 548 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 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 502 VAL 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 158 THR Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 502 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 71 optimal weight: 0.0070 chunk 142 optimal weight: 0.3980 chunk 93 optimal weight: 0.1980 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 212 optimal weight: 9.9990 chunk 108 optimal weight: 0.0030 chunk 165 optimal weight: 0.0670 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 20.0000 overall best weight: 0.1346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 294 GLN C 294 GLN D 294 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.111003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.095443 restraints weight = 42785.977| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.99 r_work: 0.3455 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 18316 Z= 0.077 Angle : 0.443 8.673 24996 Z= 0.212 Chirality : 0.035 0.147 2952 Planarity : 0.002 0.033 3068 Dihedral : 3.473 30.732 2616 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.44 % Allowed : 15.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.18), residues: 2328 helix: 2.57 (0.14), residues: 1396 sheet: 0.69 (0.53), residues: 88 loop : 0.19 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 333 HIS 0.001 0.000 HIS D 165 PHE 0.008 0.001 PHE B 407 TYR 0.008 0.001 TYR D 162 ARG 0.001 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.02627 ( 1040) hydrogen bonds : angle 3.39940 ( 3012) covalent geometry : bond 0.00150 (18316) covalent geometry : angle 0.44305 (24996) *********************** 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 216 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 1.997 Fit side-chains REVERT: A 272 ASP cc_start: 0.7958 (p0) cc_final: 0.7738 (p0) REVERT: A 634 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: A 640 MET cc_start: 0.8587 (tmm) cc_final: 0.7854 (tpt) REVERT: B 272 ASP cc_start: 0.8011 (p0) cc_final: 0.7786 (p0) REVERT: B 632 LEU cc_start: 0.7774 (mt) cc_final: 0.7501 (mp) REVERT: B 634 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: C 272 ASP cc_start: 0.8008 (p0) cc_final: 0.7781 (p0) REVERT: C 634 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: D 272 ASP cc_start: 0.7965 (p0) cc_final: 0.7708 (p0) REVERT: D 634 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: D 640 MET cc_start: 0.8578 (tmm) cc_final: 0.7876 (tpt) outliers start: 24 outliers final: 16 residues processed: 208 average time/residue: 0.2305 time to fit residues: 81.0172 Evaluate side-chains 200 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 638 LEU 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 545 LEU Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL 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 75 optimal weight: 3.9990 chunk 220 optimal weight: 0.0970 chunk 127 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 61 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.9558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 294 GLN C 294 GLN D 294 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.108738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.093007 restraints weight = 42863.112| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.99 r_work: 0.3410 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18316 Z= 0.094 Angle : 0.458 9.372 24996 Z= 0.219 Chirality : 0.035 0.156 2952 Planarity : 0.002 0.033 3068 Dihedral : 3.581 37.721 2616 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.56 % Allowed : 15.53 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.18), residues: 2328 helix: 2.68 (0.14), residues: 1396 sheet: 0.73 (0.53), residues: 88 loop : 0.27 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 223 HIS 0.001 0.000 HIS A 251 PHE 0.009 0.001 PHE B 407 TYR 0.009 0.001 TYR D 228 ARG 0.001 0.000 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.02869 ( 1040) hydrogen bonds : angle 3.43009 ( 3012) covalent geometry : bond 0.00215 (18316) covalent geometry : angle 0.45779 (24996) ********************** 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 201 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 2.193 Fit side-chains REVERT: A 272 ASP cc_start: 0.8058 (p0) cc_final: 0.7844 (p0) REVERT: A 634 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: A 640 MET cc_start: 0.8592 (tmm) cc_final: 0.7871 (tpt) REVERT: B 634 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: B 640 MET cc_start: 0.8459 (ppp) cc_final: 0.7900 (tpt) REVERT: C 634 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: D 548 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6881 (tp) REVERT: D 634 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: D 640 MET cc_start: 0.8587 (tmm) cc_final: 0.7909 (tpt) outliers start: 26 outliers final: 16 residues processed: 193 average time/residue: 0.2303 time to fit residues: 75.5525 Evaluate side-chains 192 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 502 VAL 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 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 177 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.105489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.089899 restraints weight = 43033.897| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.88 r_work: 0.3359 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18316 Z= 0.153 Angle : 0.516 10.363 24996 Z= 0.248 Chirality : 0.037 0.176 2952 Planarity : 0.003 0.033 3068 Dihedral : 3.966 45.370 2616 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.98 % Allowed : 15.17 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.18), residues: 2328 helix: 2.54 (0.14), residues: 1392 sheet: 0.39 (0.52), residues: 88 loop : 0.27 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 223 HIS 0.003 0.001 HIS C 165 PHE 0.011 0.001 PHE B 407 TYR 0.010 0.001 TYR A 162 ARG 0.002 0.000 ARG A 560 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 1040) hydrogen bonds : angle 3.62028 ( 3012) covalent geometry : bond 0.00363 (18316) covalent geometry : angle 0.51578 (24996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8715.51 seconds wall clock time: 150 minutes 15.55 seconds (9015.55 seconds total)