Starting phenix.real_space_refine on Mon May 19 03:13:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slx_40582/05_2025/8slx_40582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slx_40582/05_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_40582/05_2025/8slx_40582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slx_40582/05_2025/8slx_40582.map" model { file = "/net/cci-nas-00/data/ceres_data/8slx_40582/05_2025/8slx_40582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slx_40582/05_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-5687/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: 10.21, per 1000 atoms: 0.57 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: 4.07 Conformation dependent library (CDL) restraints added in 2.2 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: 1.94 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: 5.31 Time building geometry restraints manager: 4.72 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: 1.600 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 38.460 Find NCS groups from input model: 0.980 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.880 ------------------------------------------------------------------------------- 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 : 2.044 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: 0.2149 time to fit residues: 82.4819 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 : 1.873 ------------------------------------------------------------------------------- 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 = 0.105093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.089297 restraints weight = 43048.945| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.92 r_work: 0.3343 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 1.953 Fit side-chains REVERT: A 634 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: B 634 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: C 634 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: D 634 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.8074 (m-80) outliers start: 20 outliers final: 14 residues processed: 190 average time/residue: 0.2150 time to fit residues: 68.9469 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 : 1.814 ------------------------------------------------------------------------------- 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: 0.7980 chunk 42 optimal weight: 1.9990 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: 0.9980 chunk 143 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.108166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092734 restraints weight = 42733.911| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.90 r_work: 0.3411 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2120 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= 0.092 Angle : 0.453 6.880 24996 Z= 0.226 Chirality : 0.035 0.126 2952 Planarity : 0.003 0.032 3068 Dihedral : 4.737 68.025 2616 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.84 % Allowed : 10.73 % Favored : 88.43 % 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: 2.17 (0.18), residues: 2328 helix: 2.40 (0.14), residues: 1372 sheet: 0.49 (0.55), residues: 88 loop : -0.01 (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 D 165 PHE 0.008 0.001 PHE B 407 TYR 0.009 0.001 TYR A 162 ARG 0.003 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 1040) hydrogen bonds : angle 3.77901 ( 3012) covalent geometry : bond 0.00200 (18316) covalent geometry : angle 0.45306 (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 197 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 1.879 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 191 average time/residue: 0.2382 time to fit residues: 76.9010 Evaluate side-chains 180 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 496 TRP 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 441 ILE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain D residue 441 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 42 optimal weight: 4.9990 chunk 213 optimal weight: 0.0070 chunk 131 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.109351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.093763 restraints weight = 43023.736| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.96 r_work: 0.3424 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2310 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= 0.083 Angle : 0.435 7.085 24996 Z= 0.215 Chirality : 0.035 0.127 2952 Planarity : 0.003 0.032 3068 Dihedral : 3.984 55.050 2616 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.32 % Allowed : 11.87 % Favored : 86.81 % 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: 2.29 (0.18), residues: 2328 helix: 2.54 (0.14), residues: 1368 sheet: 0.56 (0.55), residues: 88 loop : -0.02 (0.21), residues: 872 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 0.022 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 0.02998 ( 1040) hydrogen bonds : angle 3.59170 ( 3012) covalent geometry : bond 0.00177 (18316) covalent geometry : angle 0.43515 (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 207 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 2.017 Fit side-chains REVERT: A 634 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.8138 (m-80) REVERT: B 634 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: C 634 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: D 634 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.8074 (m-80) outliers start: 22 outliers final: 13 residues processed: 198 average time/residue: 0.2211 time to fit residues: 73.6362 Evaluate side-chains 197 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 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 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 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 634 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 100 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.106502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090899 restraints weight = 43361.615| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.91 r_work: 0.3375 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18316 Z= 0.130 Angle : 0.481 9.245 24996 Z= 0.234 Chirality : 0.036 0.150 2952 Planarity : 0.003 0.033 3068 Dihedral : 4.050 50.162 2616 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.04 % Allowed : 12.05 % Favored : 85.91 % 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: 2.39 (0.18), residues: 2328 helix: 2.58 (0.14), residues: 1372 sheet: 0.47 (0.52), residues: 88 loop : 0.09 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.002 0.001 HIS A 165 PHE 0.014 0.001 PHE B 407 TYR 0.009 0.001 TYR D 162 ARG 0.002 0.000 ARG C 702 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 1040) hydrogen bonds : angle 3.64025 ( 3012) covalent geometry : bond 0.00306 (18316) covalent geometry : angle 0.48080 (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 209 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 1.929 Fit side-chains REVERT: A 634 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: B 634 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: C 634 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: D 634 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.8010 (m-80) outliers start: 34 outliers final: 23 residues processed: 194 average time/residue: 0.2203 time to fit residues: 72.7576 Evaluate side-chains 194 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 2.068 ------------------------------------------------------------------------------- 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 546 VAL Chi-restraints excluded: chain A residue 604 THR 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 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 634 TYR 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 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 546 VAL Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 630 VAL 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: 7.9990 chunk 48 optimal weight: 0.6980 chunk 162 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 233 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.108338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092775 restraints weight = 42806.519| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.96 r_work: 0.3412 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18316 Z= 0.084 Angle : 0.437 8.089 24996 Z= 0.212 Chirality : 0.035 0.135 2952 Planarity : 0.002 0.033 3068 Dihedral : 3.728 38.570 2616 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.80 % Allowed : 13.73 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.49 (0.18), residues: 2328 helix: 2.68 (0.14), residues: 1372 sheet: 0.54 (0.52), residues: 88 loop : 0.10 (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 A 313 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 0.02895 ( 1040) hydrogen bonds : angle 3.50612 ( 3012) covalent geometry : bond 0.00186 (18316) covalent geometry : angle 0.43678 (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 208 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 1.853 Fit side-chains REVERT: A 272 ASP cc_start: 0.7992 (p0) cc_final: 0.7744 (p0) REVERT: A 634 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: B 634 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: C 634 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: D 634 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7847 (m-80) outliers start: 30 outliers final: 23 residues processed: 191 average time/residue: 0.2315 time to fit residues: 74.2076 Evaluate side-chains 200 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 LEU 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 545 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 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 152 LEU 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 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: 2.9990 chunk 171 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.107746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.092104 restraints weight = 42859.851| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.94 r_work: 0.3395 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2602 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= 0.097 Angle : 0.445 8.435 24996 Z= 0.217 Chirality : 0.035 0.153 2952 Planarity : 0.002 0.033 3068 Dihedral : 3.738 38.517 2616 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.52 % Allowed : 13.91 % Favored : 83.57 % 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: 0.49 (0.52), residues: 88 loop : 0.23 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.001 0.000 HIS B 165 PHE 0.010 0.001 PHE B 407 TYR 0.008 0.001 TYR A 162 ARG 0.001 0.000 ARG A 560 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 1040) hydrogen bonds : angle 3.49418 ( 3012) covalent geometry : bond 0.00223 (18316) covalent geometry : angle 0.44479 (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 214 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 2.084 Fit side-chains REVERT: A 272 ASP cc_start: 0.7987 (p0) cc_final: 0.7715 (p0) REVERT: A 634 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: B 634 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: C 634 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: D 634 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7835 (m-80) outliers start: 42 outliers final: 34 residues processed: 196 average time/residue: 0.2294 time to fit residues: 76.0206 Evaluate side-chains 206 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 496 TRP 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 390 VAL 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 152 LEU 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 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 C residue 638 LEU 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 496 TRP Chi-restraints excluded: chain D residue 502 VAL 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: 6.9990 chunk 223 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 HIS B 413 HIS C 234 HIS C 413 HIS C 438 HIS D 413 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.103942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088375 restraints weight = 42945.271| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.89 r_work: 0.3329 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18316 Z= 0.194 Angle : 0.538 10.700 24996 Z= 0.262 Chirality : 0.037 0.176 2952 Planarity : 0.003 0.033 3068 Dihedral : 4.250 45.058 2616 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.46 % Allowed : 14.33 % Favored : 83.21 % 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: 2.27 (0.18), residues: 2328 helix: 2.45 (0.14), residues: 1372 sheet: 0.12 (0.52), residues: 88 loop : 0.16 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 715 HIS 0.004 0.001 HIS B 165 PHE 0.013 0.001 PHE B 407 TYR 0.011 0.001 TYR D 162 ARG 0.002 0.000 ARG A 560 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 1040) hydrogen bonds : angle 3.75370 ( 3012) covalent geometry : bond 0.00459 (18316) covalent geometry : angle 0.53787 (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 197 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 2.229 Fit side-chains REVERT: A 634 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: B 548 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6857 (tp) REVERT: B 634 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: C 634 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: D 634 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7741 (m-80) outliers start: 41 outliers final: 32 residues processed: 178 average time/residue: 0.2449 time to fit residues: 74.6023 Evaluate side-chains 191 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 2.108 ------------------------------------------------------------------------------- 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 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 390 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 502 VAL 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: 0.3980 chunk 142 optimal weight: 0.2980 chunk 93 optimal weight: 0.0570 chunk 147 optimal weight: 7.9990 chunk 88 optimal weight: 0.0770 chunk 91 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 chunk 118 optimal weight: 20.0000 overall best weight: 0.1834 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.109859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.094361 restraints weight = 42901.392| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.97 r_work: 0.3434 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18316 Z= 0.078 Angle : 0.438 7.698 24996 Z= 0.213 Chirality : 0.035 0.148 2952 Planarity : 0.002 0.033 3068 Dihedral : 3.597 33.585 2616 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.74 % Allowed : 15.35 % 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: 2.39 (0.18), residues: 2328 helix: 2.50 (0.14), residues: 1396 sheet: 0.39 (0.52), residues: 88 loop : 0.20 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 333 HIS 0.002 0.000 HIS D 165 PHE 0.009 0.001 PHE B 407 TYR 0.008 0.001 TYR D 228 ARG 0.001 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02736 ( 1040) hydrogen bonds : angle 3.46749 ( 3012) covalent geometry : bond 0.00157 (18316) covalent geometry : angle 0.43761 (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 208 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 1.991 Fit side-chains REVERT: A 272 ASP cc_start: 0.7995 (p0) cc_final: 0.7758 (p0) REVERT: A 634 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: B 634 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: C 634 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: D 634 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7821 (m-80) outliers start: 29 outliers final: 14 residues processed: 195 average time/residue: 0.2323 time to fit residues: 76.7909 Evaluate side-chains 193 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 2.157 ------------------------------------------------------------------------------- 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 501 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 638 LEU 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 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 D residue 390 VAL Chi-restraints excluded: chain D residue 502 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 75 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 226 optimal weight: 0.0270 chunk 126 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 overall best weight: 3.7844 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.103143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.087440 restraints weight = 43398.495| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.91 r_work: 0.3312 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18316 Z= 0.238 Angle : 0.590 11.232 24996 Z= 0.285 Chirality : 0.038 0.208 2952 Planarity : 0.003 0.032 3068 Dihedral : 4.389 51.128 2616 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.98 % Allowed : 15.23 % Favored : 82.79 % 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: 2.21 (0.18), residues: 2328 helix: 2.36 (0.14), residues: 1372 sheet: 0.04 (0.53), residues: 88 loop : 0.23 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 454 HIS 0.006 0.001 HIS B 165 PHE 0.013 0.002 PHE B 407 TYR 0.013 0.002 TYR A 162 ARG 0.003 0.001 ARG C 369 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 1040) hydrogen bonds : angle 3.85983 ( 3012) covalent geometry : bond 0.00562 (18316) covalent geometry : angle 0.59035 (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 188 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 2.031 Fit side-chains REVERT: A 634 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: B 548 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6851 (tp) REVERT: B 634 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: C 634 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: C 640 MET cc_start: 0.8452 (ppp) cc_final: 0.8130 (tpp) REVERT: D 634 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: D 640 MET cc_start: 0.8614 (tmm) cc_final: 0.8220 (tpt) outliers start: 33 outliers final: 22 residues processed: 177 average time/residue: 0.2254 time to fit residues: 68.0155 Evaluate side-chains 181 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 630 VAL 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 390 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 548 LEU 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 390 VAL 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 634 TYR 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 502 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 177 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 206 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 193 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.107049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.091589 restraints weight = 42862.579| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.89 r_work: 0.3387 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 0.031 18316 Z= 0.100 Angle : 0.478 10.116 24996 Z= 0.230 Chirality : 0.035 0.178 2952 Planarity : 0.003 0.033 3068 Dihedral : 3.890 43.035 2616 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.68 % Allowed : 15.89 % Favored : 82.43 % 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: 2.34 (0.18), residues: 2328 helix: 2.45 (0.14), residues: 1392 sheet: 0.05 (0.52), residues: 88 loop : 0.25 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 333 HIS 0.002 0.000 HIS C 165 PHE 0.009 0.001 PHE B 407 TYR 0.008 0.001 TYR D 228 ARG 0.001 0.000 ARG D 560 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 1040) hydrogen bonds : angle 3.59277 ( 3012) covalent geometry : bond 0.00227 (18316) covalent geometry : angle 0.47845 (24996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7986.69 seconds wall clock time: 139 minutes 15.93 seconds (8355.93 seconds total)