Starting phenix.real_space_refine on Mon Nov 18 23:54:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8slx_40582/11_2024/8slx_40582.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8slx_40582/11_2024/8slx_40582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8slx_40582/11_2024/8slx_40582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8slx_40582/11_2024/8slx_40582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8slx_40582/11_2024/8slx_40582.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8slx_40582/11_2024/8slx_40582.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 Na 1 4.78 5 C 11800 2.51 5 N 3012 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17885 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4447 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 18, 'TRANS': 575} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 528 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 271 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' NA': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 10.34, per 1000 atoms: 0.58 Number of scatterers: 17885 At special positions: 0 Unit cell: (155.21, 155.21, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 Na 1 11.00 O 2976 8.00 N 3012 7.00 C 11800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.82 Conformation dependent library (CDL) restraints added in 2.3 seconds 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 65.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.533A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.911A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 102 removed outlier: 4.363A pdb=" N ARG A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.763A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.699A pdb=" N HIS A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 413 Processing helix chain 'A' and resid 433 through 459 Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.813A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.925A pdb=" N ILE A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 removed outlier: 4.096A pdb=" N GLN A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 560 removed outlier: 4.010A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 650 removed outlier: 3.567A pdb=" N LEU A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.534A pdb=" N ARG B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.912A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 102 removed outlier: 4.362A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.762A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 366 through 370 removed outlier: 4.698A pdb=" N HIS B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 413 Processing helix chain 'B' and resid 433 through 459 Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.813A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.925A pdb=" N ILE B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 removed outlier: 4.096A pdb=" N GLN B 530 " --> pdb=" O SER B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 560 removed outlier: 4.011A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 650 removed outlier: 3.566A pdb=" N LEU B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER B 656 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.533A pdb=" N ARG C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.912A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 102 removed outlier: 4.363A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP C 145 " --> pdb=" O GLN C 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.763A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 366 through 370 removed outlier: 4.699A pdb=" N HIS C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 413 Processing helix chain 'C' and resid 433 through 459 Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.812A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.924A pdb=" N ILE C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 531 removed outlier: 4.097A pdb=" N GLN C 530 " --> pdb=" O SER C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 560 removed outlier: 4.010A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 650 removed outlier: 3.566A pdb=" N LEU C 623 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.533A pdb=" N ARG D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.911A pdb=" N LEU D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 102 removed outlier: 4.363A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 removed outlier: 3.628A pdb=" N ASP D 145 " --> pdb=" O GLN D 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.763A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 366 through 370 removed outlier: 4.698A pdb=" N HIS D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 389 removed outlier: 3.931A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 413 Processing helix chain 'D' and resid 433 through 459 Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.813A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.464A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 526 removed outlier: 3.925A pdb=" N ILE D 524 " --> pdb=" O GLN D 520 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 531 removed outlier: 4.097A pdb=" N GLN D 530 " --> pdb=" O SER D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 560 removed outlier: 4.010A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 650 removed outlier: 3.567A pdb=" N LEU D 623 " --> pdb=" O ARG D 619 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 673 removed outlier: 3.548A pdb=" N SER D 656 " --> pdb=" O VAL D 652 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 689 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 689 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 689 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 7.421A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 689 " --> pdb=" O ARG D 702 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 3012 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 5.18 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: 1.610 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: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 38.980 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.650 ------------------------------------------------------------------------------- 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= 0.260 Angle : 0.479 8.107 24996 Z= 0.228 Chirality : 0.041 0.617 2952 Planarity : 0.002 0.030 3068 Dihedral : 13.461 139.178 6104 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.17), residues: 2328 helix: 1.79 (0.14), residues: 1312 sheet: 0.62 (0.55), residues: 88 loop : -0.15 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 496 HIS 0.002 0.000 HIS B 165 PHE 0.011 0.001 PHE D 547 TYR 0.015 0.001 TYR D 162 ARG 0.001 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.582 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: 0.2321 time to fit residues: 88.9669 Evaluate side-chains 185 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.9990 chunk 178 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 639 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 GLN C 438 HIS C 487 GLN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18316 Z= 0.288 Angle : 0.553 7.619 24996 Z= 0.275 Chirality : 0.038 0.138 2952 Planarity : 0.003 0.033 3068 Dihedral : 6.307 96.228 2616 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.20 % Allowed : 7.67 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.18), residues: 2328 helix: 1.96 (0.14), residues: 1396 sheet: 0.67 (0.58), residues: 88 loop : -0.10 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 496 HIS 0.005 0.001 HIS B 169 PHE 0.014 0.001 PHE B 407 TYR 0.013 0.002 TYR A 162 ARG 0.003 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 2.050 Fit side-chains REVERT: A 634 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: B 634 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: C 634 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: D 634 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.8047 (m-80) outliers start: 20 outliers final: 14 residues processed: 190 average time/residue: 0.2371 time to fit residues: 76.2300 Evaluate side-chains 177 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18316 Z= 0.195 Angle : 0.485 7.448 24996 Z= 0.242 Chirality : 0.036 0.134 2952 Planarity : 0.003 0.034 3068 Dihedral : 4.831 66.855 2616 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.26 % Allowed : 10.37 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.18), residues: 2328 helix: 2.25 (0.14), residues: 1388 sheet: 0.48 (0.56), residues: 88 loop : 0.04 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 333 HIS 0.003 0.001 HIS D 165 PHE 0.010 0.001 PHE B 407 TYR 0.010 0.001 TYR A 162 ARG 0.002 0.000 ARG A 175 *********************** 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 194 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 2.101 Fit side-chains REVERT: B 496 TRP cc_start: 0.8130 (OUTLIER) cc_final: 0.7838 (t-100) outliers start: 21 outliers final: 15 residues processed: 183 average time/residue: 0.2358 time to fit residues: 72.2754 Evaluate side-chains 180 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 2.038 ------------------------------------------------------------------------------- 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 B residue 436 LEU Chi-restraints excluded: chain B residue 496 TRP Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 630 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 228 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2355 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= 0.190 Angle : 0.473 8.113 24996 Z= 0.234 Chirality : 0.035 0.138 2952 Planarity : 0.003 0.034 3068 Dihedral : 4.169 54.201 2616 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.70 % Allowed : 11.21 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.18), residues: 2328 helix: 2.44 (0.14), residues: 1372 sheet: 0.32 (0.54), residues: 88 loop : 0.05 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 333 HIS 0.003 0.001 HIS D 165 PHE 0.013 0.001 PHE B 407 TYR 0.010 0.001 TYR B 228 ARG 0.001 0.000 ARG D 560 *********************** 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 213 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 2.077 Fit side-chains REVERT: A 634 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: B 634 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: C 634 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: D 634 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7962 (m-80) outliers start: 45 outliers final: 31 residues processed: 196 average time/residue: 0.2367 time to fit residues: 78.3590 Evaluate side-chains 200 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 441 ILE 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 546 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 496 TRP Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.2980 chunk 129 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 HIS B 234 HIS B 413 HIS C 413 HIS C 438 HIS D 413 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18316 Z= 0.300 Angle : 0.537 9.657 24996 Z= 0.263 Chirality : 0.037 0.152 2952 Planarity : 0.003 0.035 3068 Dihedral : 4.365 52.769 2616 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.46 % Allowed : 12.77 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.18), residues: 2328 helix: 2.43 (0.14), residues: 1348 sheet: 0.14 (0.54), residues: 88 loop : 0.15 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 715 HIS 0.005 0.001 HIS C 165 PHE 0.012 0.001 PHE B 407 TYR 0.012 0.001 TYR D 228 ARG 0.002 0.000 ARG D 560 *********************** 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 198 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 2.123 Fit side-chains REVERT: A 634 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: B 634 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: C 634 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: D 634 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7866 (m-80) outliers start: 41 outliers final: 31 residues processed: 178 average time/residue: 0.2380 time to fit residues: 71.9273 Evaluate side-chains 188 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 2.201 ------------------------------------------------------------------------------- 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 441 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 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 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 152 LEU Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 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 158 THR Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 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 76 optimal weight: 0.0000 chunk 205 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 228 optimal weight: 0.8980 chunk 189 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18316 Z= 0.135 Angle : 0.446 7.465 24996 Z= 0.219 Chirality : 0.035 0.135 2952 Planarity : 0.003 0.034 3068 Dihedral : 3.906 45.768 2616 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.58 % Allowed : 13.37 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.18), residues: 2328 helix: 2.53 (0.14), residues: 1368 sheet: 0.11 (0.53), residues: 88 loop : 0.09 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 333 HIS 0.002 0.000 HIS C 165 PHE 0.008 0.001 PHE B 407 TYR 0.009 0.001 TYR B 228 ARG 0.001 0.000 ARG D 560 *********************** 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 215 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 2.090 Fit side-chains REVERT: A 634 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: B 634 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: C 634 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: D 634 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7850 (m-80) outliers start: 43 outliers final: 33 residues processed: 195 average time/residue: 0.2386 time to fit residues: 77.9805 Evaluate side-chains 211 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 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 234 HIS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 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 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 158 THR 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 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 220 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2630 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= 0.149 Angle : 0.462 9.005 24996 Z= 0.224 Chirality : 0.035 0.150 2952 Planarity : 0.003 0.034 3068 Dihedral : 3.892 44.478 2616 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.76 % Allowed : 14.03 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.18), residues: 2328 helix: 2.47 (0.14), residues: 1396 sheet: 0.16 (0.52), residues: 88 loop : 0.25 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 333 HIS 0.002 0.001 HIS C 165 PHE 0.012 0.001 PHE B 407 TYR 0.009 0.001 TYR D 228 ARG 0.001 0.000 ARG B 560 *********************** 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 222 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 2.153 Fit side-chains REVERT: A 634 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 548 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6850 (tp) REVERT: B 634 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: B 639 ASN cc_start: 0.8363 (t0) cc_final: 0.8123 (t0) REVERT: C 634 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: D 634 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7841 (m-80) outliers start: 46 outliers final: 36 residues processed: 203 average time/residue: 0.2372 time to fit residues: 81.5575 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 : 2.022 ------------------------------------------------------------------------------- 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 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 604 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 496 TRP 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 158 THR Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 501 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 140 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 0.0050 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 144 optimal weight: 0.0370 chunk 154 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 206 optimal weight: 0.9990 overall best weight: 0.5274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 294 GLN C 294 GLN D 294 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18316 Z= 0.110 Angle : 0.442 9.065 24996 Z= 0.214 Chirality : 0.035 0.150 2952 Planarity : 0.002 0.034 3068 Dihedral : 3.672 39.824 2616 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.28 % Allowed : 14.45 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.18), residues: 2328 helix: 2.52 (0.14), residues: 1392 sheet: 0.37 (0.52), residues: 88 loop : 0.25 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 333 HIS 0.001 0.000 HIS B 438 PHE 0.017 0.001 PHE B 407 TYR 0.008 0.001 TYR B 228 ARG 0.001 0.000 ARG B 490 *********************** 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 218 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 2.141 Fit side-chains REVERT: A 272 ASP cc_start: 0.7815 (p0) cc_final: 0.7599 (p0) REVERT: A 634 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: B 272 ASP cc_start: 0.7792 (p0) cc_final: 0.7536 (p0) REVERT: B 634 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: C 634 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: D 634 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7776 (m-80) outliers start: 38 outliers final: 27 residues processed: 209 average time/residue: 0.2341 time to fit residues: 82.7877 Evaluate side-chains 198 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 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 604 THR Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 496 TRP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 604 THR 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 158 THR Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 546 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 294 GLN C 294 GLN D 294 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18316 Z= 0.168 Angle : 0.473 9.718 24996 Z= 0.228 Chirality : 0.035 0.159 2952 Planarity : 0.003 0.034 3068 Dihedral : 3.833 43.340 2616 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.82 % Allowed : 14.39 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.18), residues: 2328 helix: 2.52 (0.14), residues: 1396 sheet: 0.27 (0.52), residues: 88 loop : 0.29 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 333 HIS 0.002 0.001 HIS B 165 PHE 0.019 0.001 PHE B 407 TYR 0.009 0.001 TYR D 228 ARG 0.001 0.000 ARG A 560 *********************** 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: 47 poor density : 166 time to evaluate : 1.857 Fit side-chains REVERT: A 272 ASP cc_start: 0.7827 (p0) cc_final: 0.7592 (p0) REVERT: A 634 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: B 634 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: C 634 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: D 548 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6774 (tp) REVERT: D 634 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: D 640 MET cc_start: 0.8240 (tmm) cc_final: 0.8023 (tpt) outliers start: 47 outliers final: 33 residues processed: 201 average time/residue: 0.2270 time to fit residues: 77.4937 Evaluate side-chains 201 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 2.039 ------------------------------------------------------------------------------- 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 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 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 633 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 234 HIS 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 604 THR 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 158 THR Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR 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 136 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 235 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18316 Z= 0.150 Angle : 0.469 10.081 24996 Z= 0.227 Chirality : 0.035 0.162 2952 Planarity : 0.003 0.034 3068 Dihedral : 3.789 42.406 2616 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.46 % Allowed : 14.99 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.18), residues: 2328 helix: 2.54 (0.14), residues: 1396 sheet: 0.28 (0.52), residues: 88 loop : 0.27 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 333 HIS 0.002 0.000 HIS C 165 PHE 0.018 0.001 PHE B 407 TYR 0.008 0.001 TYR B 228 ARG 0.001 0.000 ARG A 560 ********************** 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 210 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 1.997 Fit side-chains REVERT: A 272 ASP cc_start: 0.7817 (p0) cc_final: 0.7583 (p0) REVERT: A 634 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: B 272 ASP cc_start: 0.7855 (p0) cc_final: 0.7616 (p0) REVERT: B 634 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: C 272 ASP cc_start: 0.7823 (p0) cc_final: 0.7587 (p0) REVERT: C 528 MET cc_start: 0.8006 (mtm) cc_final: 0.7626 (mtm) REVERT: C 634 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: D 548 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6786 (tp) REVERT: D 634 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: D 640 MET cc_start: 0.8235 (tmm) cc_final: 0.7988 (tpt) outliers start: 41 outliers final: 34 residues processed: 196 average time/residue: 0.2356 time to fit residues: 78.0686 Evaluate side-chains 206 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 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 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 436 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 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 158 THR Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 634 TYR 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 57 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 192 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 294 GLN C 294 GLN D 294 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.108876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093375 restraints weight = 42518.835| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.93 r_work: 0.3419 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18316 Z= 0.120 Angle : 0.452 9.857 24996 Z= 0.218 Chirality : 0.035 0.148 2952 Planarity : 0.003 0.035 3068 Dihedral : 3.625 38.713 2616 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.16 % Allowed : 15.71 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.18), residues: 2328 helix: 2.59 (0.14), residues: 1396 sheet: 0.41 (0.52), residues: 88 loop : 0.16 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 333 HIS 0.002 0.000 HIS B 438 PHE 0.016 0.001 PHE B 407 TYR 0.008 0.001 TYR D 228 ARG 0.001 0.000 ARG D 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3177.04 seconds wall clock time: 59 minutes 15.84 seconds (3555.84 seconds total)