Starting phenix.real_space_refine on Sat Oct 11 21:09:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slx_40582/10_2025/8slx_40582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slx_40582/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8slx_40582/10_2025/8slx_40582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slx_40582/10_2025/8slx_40582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8slx_40582/10_2025/8slx_40582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slx_40582/10_2025/8slx_40582.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 Na 1 4.78 5 C 11800 2.51 5 N 3012 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'PHE:plan': 3, 'ASP:plan': 12, 'ARG:plan': 12, 'GLU:plan': 20, 'TYR:plan': 3, 'TRP:plan': 2, 'GLN:plan1': 6, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 271 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' NA': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.65, per 1000 atoms: 0.26 Number of scatterers: 17885 At special positions: 0 Unit cell: (155.21, 155.21, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 Na 1 11.00 O 2976 8.00 N 3012 7.00 C 11800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 65.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.533A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.911A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 102 removed outlier: 4.363A pdb=" N ARG A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.763A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.699A pdb=" N HIS A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 413 Processing helix chain 'A' and resid 433 through 459 Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.813A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.925A pdb=" N ILE A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 removed outlier: 4.096A pdb=" N GLN A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 560 removed outlier: 4.010A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 650 removed outlier: 3.567A pdb=" N LEU A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.534A pdb=" N ARG B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.912A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 102 removed outlier: 4.362A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.762A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 366 through 370 removed outlier: 4.698A pdb=" N HIS B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 413 Processing helix chain 'B' and resid 433 through 459 Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.813A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.925A pdb=" N ILE B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 removed outlier: 4.096A pdb=" N GLN B 530 " --> pdb=" O SER B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 560 removed outlier: 4.011A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 650 removed outlier: 3.566A pdb=" N LEU B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER B 656 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.533A pdb=" N ARG C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.912A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 102 removed outlier: 4.363A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP C 145 " --> pdb=" O GLN C 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.763A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 366 through 370 removed outlier: 4.699A pdb=" N HIS C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 413 Processing helix chain 'C' and resid 433 through 459 Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.812A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.924A pdb=" N ILE C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 531 removed outlier: 4.097A pdb=" N GLN C 530 " --> pdb=" O SER C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 560 removed outlier: 4.010A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 650 removed outlier: 3.566A pdb=" N LEU C 623 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.533A pdb=" N ARG D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.911A pdb=" N LEU D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 102 removed outlier: 4.363A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP D 145 " --> pdb=" O GLN D 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.763A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 366 through 370 removed outlier: 4.698A pdb=" N HIS D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 413 Processing helix chain 'D' and resid 433 through 459 Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.813A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 526 removed outlier: 3.925A pdb=" N ILE D 524 " --> pdb=" O GLN D 520 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 531 removed outlier: 4.097A pdb=" N GLN D 530 " --> pdb=" O SER D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 560 removed outlier: 4.010A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 650 removed outlier: 3.567A pdb=" N LEU D 623 " --> pdb=" O ARG D 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER D 656 " --> pdb=" O VAL D 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 689 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 689 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 689 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 689 " --> pdb=" O ARG D 702 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 3012 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 2.50 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: 1.930 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.950 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.17), residues: 2328 helix: 1.79 (0.14), residues: 1312 sheet: 0.62 (0.55), residues: 88 loop : -0.15 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 560 TYR 0.015 0.001 TYR D 162 PHE 0.011 0.001 PHE D 547 TRP 0.005 0.001 TRP A 496 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00400 (18316) covalent geometry : angle 0.47869 (24996) hydrogen bonds : bond 0.25001 ( 1040) hydrogen bonds : angle 6.39841 ( 3012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.755 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: 0.1020 time to fit residues: 39.6793 Evaluate side-chains 185 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 487 GLN A 639 ASN B 294 GLN B 487 GLN B 639 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 GLN C 438 HIS C 487 GLN C 639 ASN D 294 GLN D 487 GLN D 639 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.109164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.093722 restraints weight = 43102.855| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.89 r_work: 0.3428 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1643 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= 0.105 Angle : 0.477 6.904 24996 Z= 0.239 Chirality : 0.036 0.141 2952 Planarity : 0.003 0.031 3068 Dihedral : 6.245 97.158 2616 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.84 % Allowed : 6.35 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.17), residues: 2328 helix: 2.15 (0.14), residues: 1392 sheet: 0.65 (0.56), residues: 88 loop : -0.09 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 702 TYR 0.012 0.001 TYR A 162 PHE 0.013 0.001 PHE D 407 TRP 0.006 0.001 TRP C 509 HIS 0.003 0.000 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00227 (18316) covalent geometry : angle 0.47677 (24996) hydrogen bonds : bond 0.03836 ( 1040) hydrogen bonds : angle 4.04645 ( 3012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.606 Fit side-chains REVERT: A 272 ASP cc_start: 0.8001 (p0) cc_final: 0.7776 (p0) outliers start: 14 outliers final: 10 residues processed: 205 average time/residue: 0.1095 time to fit residues: 38.1710 Evaluate side-chains 185 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 630 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 107 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.106558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.090919 restraints weight = 43510.060| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.94 r_work: 0.3373 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18316 Z= 0.131 Angle : 0.483 7.498 24996 Z= 0.240 Chirality : 0.036 0.148 2952 Planarity : 0.003 0.033 3068 Dihedral : 4.701 65.151 2616 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.14 % Allowed : 10.01 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.18), residues: 2328 helix: 2.40 (0.14), residues: 1372 sheet: 0.58 (0.56), residues: 88 loop : 0.00 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 702 TYR 0.010 0.001 TYR A 162 PHE 0.019 0.001 PHE C 601 TRP 0.008 0.001 TRP C 496 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00306 (18316) covalent geometry : angle 0.48254 (24996) hydrogen bonds : bond 0.03622 ( 1040) hydrogen bonds : angle 3.84700 ( 3012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.722 Fit side-chains REVERT: A 634 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: B 634 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: C 634 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: D 634 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.8132 (m-80) outliers start: 19 outliers final: 13 residues processed: 190 average time/residue: 0.1101 time to fit residues: 35.8709 Evaluate side-chains 185 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 496 TRP 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 546 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 123 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 226 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 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 = 0.3771 r_free = 0.3771 target = 0.105741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.090165 restraints weight = 43448.523| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.93 r_work: 0.3364 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18316 Z= 0.137 Angle : 0.484 8.187 24996 Z= 0.239 Chirality : 0.036 0.137 2952 Planarity : 0.003 0.033 3068 Dihedral : 4.110 49.807 2616 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.92 % Allowed : 11.81 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.18), residues: 2328 helix: 2.46 (0.14), residues: 1372 sheet: 0.40 (0.54), residues: 88 loop : 0.07 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 369 TYR 0.010 0.001 TYR A 162 PHE 0.013 0.001 PHE C 407 TRP 0.006 0.001 TRP A 496 HIS 0.003 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00324 (18316) covalent geometry : angle 0.48364 (24996) hydrogen bonds : bond 0.03353 ( 1040) hydrogen bonds : angle 3.79008 ( 3012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.762 Fit side-chains REVERT: A 634 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: B 634 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: C 634 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: D 634 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7804 (m-80) outliers start: 32 outliers final: 21 residues processed: 183 average time/residue: 0.1093 time to fit residues: 34.2630 Evaluate side-chains 190 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 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 546 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 167 optimal weight: 0.0870 chunk 231 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.107320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091845 restraints weight = 43262.261| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.90 r_work: 0.3396 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2448 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 8.160 24996 Z= 0.221 Chirality : 0.035 0.138 2952 Planarity : 0.003 0.033 3068 Dihedral : 3.861 45.863 2616 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.04 % Allowed : 12.77 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.18), residues: 2328 helix: 2.59 (0.14), residues: 1372 sheet: 0.45 (0.52), residues: 88 loop : 0.09 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 702 TYR 0.008 0.001 TYR A 162 PHE 0.009 0.001 PHE D 407 TRP 0.006 0.001 TRP D 333 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00228 (18316) covalent geometry : angle 0.45406 (24996) hydrogen bonds : bond 0.03055 ( 1040) hydrogen bonds : angle 3.59915 ( 3012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.680 Fit side-chains REVERT: A 272 ASP cc_start: 0.8041 (p0) cc_final: 0.7804 (p0) REVERT: A 634 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: B 634 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: C 634 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: D 634 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7810 (m-80) outliers start: 34 outliers final: 28 residues processed: 201 average time/residue: 0.1051 time to fit residues: 36.2300 Evaluate side-chains 208 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 545 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 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 152 LEU 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 545 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 496 TRP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 187 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 206 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 438 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.105419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.089792 restraints weight = 42790.806| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.91 r_work: 0.3357 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18316 Z= 0.140 Angle : 0.485 7.628 24996 Z= 0.237 Chirality : 0.036 0.149 2952 Planarity : 0.003 0.034 3068 Dihedral : 4.027 47.042 2616 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.64 % Allowed : 13.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.18), residues: 2328 helix: 2.53 (0.14), residues: 1372 sheet: 0.32 (0.53), residues: 88 loop : 0.13 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 560 TYR 0.009 0.001 TYR B 228 PHE 0.021 0.001 PHE B 407 TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00330 (18316) covalent geometry : angle 0.48489 (24996) hydrogen bonds : bond 0.03293 ( 1040) hydrogen bonds : angle 3.66358 ( 3012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.627 Fit side-chains REVERT: A 634 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: B 634 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: C 634 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: D 634 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7766 (m-80) outliers start: 44 outliers final: 36 residues processed: 195 average time/residue: 0.1051 time to fit residues: 34.8770 Evaluate side-chains 204 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 545 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 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 152 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 201 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 208 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS B 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.105293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089727 restraints weight = 43263.281| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.90 r_work: 0.3356 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2603 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= 0.137 Angle : 0.484 8.276 24996 Z= 0.236 Chirality : 0.036 0.157 2952 Planarity : 0.003 0.034 3068 Dihedral : 4.019 46.194 2616 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.82 % Allowed : 13.67 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.18), residues: 2328 helix: 2.53 (0.14), residues: 1372 sheet: 0.27 (0.53), residues: 88 loop : 0.16 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 560 TYR 0.009 0.001 TYR D 228 PHE 0.016 0.001 PHE C 407 TRP 0.006 0.001 TRP D 333 HIS 0.003 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00325 (18316) covalent geometry : angle 0.48377 (24996) hydrogen bonds : bond 0.03255 ( 1040) hydrogen bonds : angle 3.64576 ( 3012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.738 Fit side-chains REVERT: A 634 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: B 548 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6895 (tp) REVERT: B 634 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: C 634 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: D 634 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7753 (m-80) outliers start: 47 outliers final: 36 residues processed: 202 average time/residue: 0.1070 time to fit residues: 36.9888 Evaluate side-chains 211 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 545 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 604 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 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 172 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 200 optimal weight: 0.0670 chunk 136 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 overall best weight: 2.9524 ------------------------------------------------------------------------------- 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 413 HIS D 234 HIS D 413 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.103584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.088014 restraints weight = 43145.459| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.87 r_work: 0.3324 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18316 Z= 0.190 Angle : 0.532 8.431 24996 Z= 0.260 Chirality : 0.037 0.173 2952 Planarity : 0.003 0.034 3068 Dihedral : 4.291 48.995 2616 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.94 % Allowed : 13.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.18), residues: 2328 helix: 2.49 (0.14), residues: 1348 sheet: 0.10 (0.54), residues: 88 loop : 0.19 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 560 TYR 0.011 0.001 TYR C 228 PHE 0.016 0.001 PHE B 407 TRP 0.006 0.001 TRP C 333 HIS 0.004 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00450 (18316) covalent geometry : angle 0.53153 (24996) hydrogen bonds : bond 0.03562 ( 1040) hydrogen bonds : angle 3.78202 ( 3012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 0.765 Fit side-chains REVERT: A 634 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: B 548 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6856 (tp) REVERT: B 634 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: C 548 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6846 (tp) REVERT: C 634 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7774 (m-80) REVERT: D 548 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6778 (tp) REVERT: D 634 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7798 (m-80) outliers start: 49 outliers final: 35 residues processed: 188 average time/residue: 0.1088 time to fit residues: 34.8764 Evaluate side-chains 201 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 545 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 545 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 548 LEU 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 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 548 LEU Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 141 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.106088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.090511 restraints weight = 43002.098| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.95 r_work: 0.3368 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18316 Z= 0.108 Angle : 0.468 8.433 24996 Z= 0.228 Chirality : 0.035 0.161 2952 Planarity : 0.003 0.035 3068 Dihedral : 3.946 43.852 2616 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.00 % Allowed : 13.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.18), residues: 2328 helix: 2.51 (0.14), residues: 1372 sheet: 0.01 (0.53), residues: 88 loop : 0.20 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 684 TYR 0.009 0.001 TYR B 228 PHE 0.019 0.001 PHE B 601 TRP 0.007 0.001 TRP D 333 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00249 (18316) covalent geometry : angle 0.46786 (24996) hydrogen bonds : bond 0.03127 ( 1040) hydrogen bonds : angle 3.61137 ( 3012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 0.764 Fit side-chains REVERT: A 548 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6857 (tp) REVERT: A 634 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: B 548 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6853 (tp) REVERT: B 634 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: C 634 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: D 548 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6822 (tp) REVERT: D 634 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7746 (m-80) outliers start: 50 outliers final: 40 residues processed: 196 average time/residue: 0.1102 time to fit residues: 37.0062 Evaluate side-chains 208 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 501 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 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 234 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 545 LEU 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 689 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 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 604 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 689 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 93 optimal weight: 0.6980 chunk 206 optimal weight: 0.0870 chunk 18 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 61 optimal weight: 0.1980 chunk 229 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN C 294 GLN D 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.109066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093511 restraints weight = 42617.204| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.96 r_work: 0.3418 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2791 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= 0.080 Angle : 0.450 9.707 24996 Z= 0.216 Chirality : 0.035 0.165 2952 Planarity : 0.003 0.035 3068 Dihedral : 3.645 38.301 2616 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.92 % Allowed : 15.05 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.18), residues: 2328 helix: 2.64 (0.14), residues: 1372 sheet: 0.24 (0.52), residues: 88 loop : 0.12 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 684 TYR 0.008 0.001 TYR D 228 PHE 0.018 0.001 PHE B 601 TRP 0.008 0.001 TRP D 333 HIS 0.001 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00169 (18316) covalent geometry : angle 0.44981 (24996) hydrogen bonds : bond 0.02806 ( 1040) hydrogen bonds : angle 3.48408 ( 3012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.727 Fit side-chains REVERT: A 548 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6819 (tp) REVERT: A 634 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: B 634 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: C 634 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: D 634 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7789 (m-80) outliers start: 32 outliers final: 24 residues processed: 212 average time/residue: 0.1117 time to fit residues: 40.4293 Evaluate side-chains 199 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 501 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 689 LEU 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 634 TYR Chi-restraints excluded: chain C residue 689 LEU 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 604 THR Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 689 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 15 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 ASN C 294 GLN C 639 ASN D 294 GLN D 639 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.108362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.092758 restraints weight = 42546.051| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.94 r_work: 0.3404 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18316 Z= 0.091 Angle : 0.459 9.873 24996 Z= 0.220 Chirality : 0.035 0.166 2952 Planarity : 0.003 0.036 3068 Dihedral : 3.687 38.532 2616 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.40 % Allowed : 14.15 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.18), residues: 2328 helix: 2.69 (0.14), residues: 1372 sheet: 0.32 (0.52), residues: 88 loop : 0.22 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 560 TYR 0.008 0.001 TYR D 228 PHE 0.021 0.001 PHE D 407 TRP 0.006 0.001 TRP C 333 HIS 0.001 0.000 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00206 (18316) covalent geometry : angle 0.45940 (24996) hydrogen bonds : bond 0.02909 ( 1040) hydrogen bonds : angle 3.46659 ( 3012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4102.62 seconds wall clock time: 71 minutes 9.55 seconds (4269.55 seconds total)