Starting phenix.real_space_refine on Fri Sep 11 15:29:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6e1o_8959/09_2026/6e1o_8959.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e1o_8959/09_2026/6e1o_8959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6e1o_8959/09_2026/6e1o_8959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e1o_8959/09_2026/6e1o_8959.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6e1o_8959/09_2026/6e1o_8959.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6e1o_8959/09_2026/6e1o_8959.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e1o_8959/09_2026/6e1o_8959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e1o_8959/09_2026/6e1o_8959.map" } resolution = 3.59 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= 0.007 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 Ca 4 9.91 5 S 38 5.16 5 C 6482 2.51 5 N 1592 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9784 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4808 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 563} Chain breaks: 8 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 4808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4808 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 563} Chain breaks: 8 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CA': 2, '8K6': 1, 'D10': 1, 'D12': 4, 'HEX': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CA': 2, '8K6': 1, 'D10': 1, 'D12': 4, 'HEX': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 1.86, per 1000 atoms: 0.19 Number of scatterers: 9784 At special positions: 0 Unit cell: (132.628, 75.6309, 103.033, 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) Ca 4 19.99 S 38 16.00 O 1668 8.00 N 1592 7.00 C 6482 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: 0.86 Conformation dependent library (CDL) restraints added in 301.7 milliseconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 66.8% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.902A pdb=" N GLU B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 86 removed outlier: 3.571A pdb=" N ARG B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 117 removed outlier: 3.529A pdb=" N ILE B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 117 " --> pdb=" O HIS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.557A pdb=" N GLN B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.573A pdb=" N ARG B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.712A pdb=" N CYS B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 221 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.835A pdb=" N MET B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 308 removed outlier: 3.538A pdb=" N PHE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 305 " --> pdb=" O CYS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 348 removed outlier: 4.355A pdb=" N THR B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.554A pdb=" N ALA B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 373 removed outlier: 3.654A pdb=" N TYR B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 372 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 383 removed outlier: 4.645A pdb=" N THR B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.671A pdb=" N PHE B 433 " --> pdb=" O GLN B 429 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 446 removed outlier: 3.635A pdb=" N PHE B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 459 removed outlier: 3.684A pdb=" N ARG B 457 " --> pdb=" O GLN B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.710A pdb=" N ARG B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 525 removed outlier: 4.390A pdb=" N GLU B 514 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 520 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 522 " --> pdb=" O GLN B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 553 removed outlier: 3.561A pdb=" N ASN B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 542 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 552 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 591 removed outlier: 4.364A pdb=" N ASP B 571 " --> pdb=" O GLY B 567 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 633 removed outlier: 3.581A pdb=" N ILE B 623 " --> pdb=" O HIS B 619 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 627 " --> pdb=" O ILE B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 656 removed outlier: 3.845A pdb=" N GLU B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 644 " --> pdb=" O THR B 640 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU B 646 " --> pdb=" O ARG B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 722 removed outlier: 3.700A pdb=" N VAL B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY B 719 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 721 " --> pdb=" O GLU B 717 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 722 " --> pdb=" O VAL B 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.902A pdb=" N GLU A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.572A pdb=" N ARG A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.529A pdb=" N ILE A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 removed outlier: 3.558A pdb=" N GLN A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 172 removed outlier: 3.573A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.711A pdb=" N CYS A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.834A pdb=" N MET A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 308 removed outlier: 3.538A pdb=" N PHE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 305 " --> pdb=" O CYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 348 removed outlier: 4.355A pdb=" N THR A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.555A pdb=" N ALA A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 373 removed outlier: 3.655A pdb=" N TYR A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 4.645A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 435 removed outlier: 3.670A pdb=" N PHE A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.634A pdb=" N PHE A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 459 removed outlier: 3.684A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.709A pdb=" N ARG A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 525 removed outlier: 4.390A pdb=" N GLU A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 520 " --> pdb=" O CYS A 516 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 521 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.561A pdb=" N ASN A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 591 removed outlier: 4.362A pdb=" N ASP A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 575 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 633 removed outlier: 3.581A pdb=" N ILE A 623 " --> pdb=" O HIS A 619 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 627 " --> pdb=" O ILE A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 656 removed outlier: 3.845A pdb=" N GLU A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 644 " --> pdb=" O THR A 640 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 646 " --> pdb=" O ARG A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 722 removed outlier: 3.700A pdb=" N VAL A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 721 " --> pdb=" O GLU A 717 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 21 removed outlier: 6.756A pdb=" N TYR B 18 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG B 65 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE B 20 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHE B 63 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL B 62 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL B 52 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL B 64 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR B 50 " --> pdb=" O VAL B 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 6.757A pdb=" N TYR A 18 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG A 65 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE A 20 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHE A 63 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL A 62 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL A 52 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL A 64 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A 50 " --> pdb=" O VAL A 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 448 hydrogen bonds defined for protein. 1332 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: 1.28 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2936 1.34 - 1.46: 2238 1.46 - 1.57: 4786 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10016 Sorted by residual: bond pdb=" N VAL B 588 " pdb=" CA VAL B 588 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.21e-02 6.83e+03 7.42e+00 bond pdb=" N LEU B 524 " pdb=" CA LEU B 524 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.16e+00 bond pdb=" N LEU A 524 " pdb=" CA LEU A 524 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.05e+00 bond pdb=" N VAL A 588 " pdb=" CA VAL A 588 " ideal model delta sigma weight residual 1.460 1.491 -0.032 1.21e-02 6.83e+03 6.95e+00 bond pdb=" N MET B 590 " pdb=" CA MET B 590 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.48e+00 ... (remaining 10011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 12565 1.99 - 3.97: 698 3.97 - 5.96: 171 5.96 - 7.94: 80 7.94 - 9.93: 24 Bond angle restraints: 13538 Sorted by residual: angle pdb=" C ILE B 447 " pdb=" N VAL B 448 " pdb=" CA VAL B 448 " ideal model delta sigma weight residual 120.24 123.31 -3.07 6.30e-01 2.52e+00 2.37e+01 angle pdb=" C ILE A 447 " pdb=" N VAL A 448 " pdb=" CA VAL A 448 " ideal model delta sigma weight residual 120.24 123.27 -3.03 6.30e-01 2.52e+00 2.32e+01 angle pdb=" N VAL B 52 " pdb=" CA VAL B 52 " pdb=" C VAL B 52 " ideal model delta sigma weight residual 109.34 101.04 8.30 2.08e+00 2.31e-01 1.59e+01 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 109.34 101.08 8.26 2.08e+00 2.31e-01 1.58e+01 angle pdb=" CA VAL A 393 " pdb=" C VAL A 393 " pdb=" N PRO A 394 " ideal model delta sigma weight residual 118.88 124.94 -6.06 1.54e+00 4.22e-01 1.55e+01 ... (remaining 13533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 5367 14.33 - 28.66: 411 28.66 - 42.99: 129 42.99 - 57.32: 13 57.32 - 71.65: 6 Dihedral angle restraints: 5926 sinusoidal: 2426 harmonic: 3500 Sorted by residual: dihedral pdb=" CA THR A 127 " pdb=" C THR A 127 " pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA THR B 127 " pdb=" C THR B 127 " pdb=" N PRO B 128 " pdb=" CA PRO B 128 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ARG B 129 " pdb=" C ARG B 129 " pdb=" N HIS B 130 " pdb=" CA HIS B 130 " ideal model delta harmonic sigma weight residual -180.00 -153.58 -26.42 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 5923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 963 0.053 - 0.107: 423 0.107 - 0.160: 97 0.160 - 0.213: 21 0.213 - 0.266: 8 Chirality restraints: 1512 Sorted by residual: chirality pdb=" CB VAL B 117 " pdb=" CA VAL B 117 " pdb=" CG1 VAL B 117 " pdb=" CG2 VAL B 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL A 117 " pdb=" CA VAL A 117 " pdb=" CG1 VAL A 117 " pdb=" CG2 VAL A 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA THR B 29 " pdb=" N THR B 29 " pdb=" C THR B 29 " pdb=" CB THR B 29 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1509 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 578 " -0.019 2.00e-02 2.50e+03 1.96e-02 9.56e+00 pdb=" CG TRP A 578 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 578 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 578 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 578 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 578 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 578 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 578 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 578 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 578 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 578 " 0.019 2.00e-02 2.50e+03 1.93e-02 9.36e+00 pdb=" CG TRP B 578 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 578 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 578 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 578 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 578 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 578 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 578 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 578 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 578 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 127 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.92e+00 pdb=" N PRO A 128 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 128 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 128 " 0.041 5.00e-02 4.00e+02 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1670 2.75 - 3.29: 9237 3.29 - 3.83: 15243 3.83 - 4.36: 18079 4.36 - 4.90: 29949 Nonbonded interactions: 74178 Sorted by model distance: nonbonded pdb=" OH TYR B 589 " pdb=" O ILE B 605 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR A 589 " pdb=" O ILE A 605 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR A 506 " pdb=" OD2 ASP A 511 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR B 506 " pdb=" OD2 ASP B 511 " model vdw 2.302 3.040 nonbonded pdb=" O SER B 374 " pdb=" OH TYR B 521 " model vdw 2.314 3.040 ... (remaining 74173 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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 group one per residue 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: 1.070 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.510 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.008 0.079 10016 Z= 0.358 Angle : 1.210 9.928 13538 Z= 0.609 Chirality : 0.063 0.266 1512 Planarity : 0.008 0.075 1662 Dihedral : 11.661 71.647 3642 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.78 % Allowed : 5.38 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.85 (0.17), residues: 1146 helix: -4.19 (0.09), residues: 712 sheet: -3.24 (1.00), residues: 22 loop : -2.92 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 557 TYR 0.036 0.003 TYR A 385 PHE 0.030 0.003 PHE B 208 TRP 0.051 0.004 TRP A 578 HIS 0.007 0.003 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00815 / 0.36 (10016) covalent geometry : angle 1.20996 / 0.61 (13538) hydrogen bonds : bond 0.31465 / 19.94 ( 448) hydrogen bonds : angle 10.46344 / 7.09 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 CYS cc_start: 0.7378 (m) cc_final: 0.7118 (m) REVERT: B 515 MET cc_start: 0.8764 (mmm) cc_final: 0.8527 (mmt) REVERT: B 535 SER cc_start: 0.9568 (m) cc_final: 0.9254 (p) REVERT: B 564 ASP cc_start: 0.8417 (p0) cc_final: 0.7954 (t0) REVERT: B 607 CYS cc_start: 0.7462 (p) cc_final: 0.6966 (m) REVERT: B 616 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: B 618 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8672 (tm-30) REVERT: B 639 ASN cc_start: 0.8904 (m110) cc_final: 0.8551 (m-40) REVERT: A 151 CYS cc_start: 0.7339 (m) cc_final: 0.7091 (m) REVERT: A 515 MET cc_start: 0.8775 (mmm) cc_final: 0.8516 (mmt) REVERT: A 535 SER cc_start: 0.9558 (m) cc_final: 0.9255 (p) REVERT: A 564 ASP cc_start: 0.8438 (p0) cc_final: 0.7945 (t0) REVERT: A 618 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8670 (tm-30) REVERT: A 639 ASN cc_start: 0.8866 (m110) cc_final: 0.8565 (m-40) outliers start: 8 outliers final: 1 residues processed: 210 average time/residue: 0.1071 time to fit residues: 30.3612 Evaluate side-chains 80 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 615 PHE Chi-restraints excluded: chain B residue 616 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 ASN B 150 GLN B 230 GLN A 148 ASN A 150 GLN A 230 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.099296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084394 restraints weight = 22943.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.086580 restraints weight = 12130.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.087969 restraints weight = 7981.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088767 restraints weight = 6096.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089403 restraints weight = 5182.254| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10016 Z= 0.134 Angle : 0.697 11.771 13538 Z= 0.355 Chirality : 0.043 0.264 1512 Planarity : 0.006 0.058 1662 Dihedral : 8.414 58.347 1422 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.03 % Allowed : 11.06 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.20), residues: 1146 helix: -2.27 (0.15), residues: 764 sheet: -3.04 (0.96), residues: 22 loop : -3.17 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 644 TYR 0.014 0.002 TYR A 187 PHE 0.018 0.002 PHE A 160 TRP 0.022 0.002 TRP B 578 HIS 0.002 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10016) covalent geometry : angle 0.69705 / 0.36 (13538) hydrogen bonds : bond 0.04956 / 3.18 ( 448) hydrogen bonds : angle 4.34104 / 2.99 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.380 Fit side-chains REVERT: B 22 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: B 233 ASP cc_start: 0.8538 (t0) cc_final: 0.8302 (t0) REVERT: B 564 ASP cc_start: 0.8271 (p0) cc_final: 0.8064 (t0) REVERT: A 233 ASP cc_start: 0.8479 (t0) cc_final: 0.8228 (t0) REVERT: A 564 ASP cc_start: 0.8270 (p0) cc_final: 0.7981 (t0) REVERT: A 650 MET cc_start: 0.9032 (tmm) cc_final: 0.8812 (tmm) outliers start: 31 outliers final: 10 residues processed: 135 average time/residue: 0.0667 time to fit residues: 14.2636 Evaluate side-chains 81 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 247 HIS A 23 ASN A 247 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.082993 restraints weight = 23368.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.085114 restraints weight = 12374.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.086510 restraints weight = 8175.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087319 restraints weight = 6220.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087951 restraints weight = 5278.376| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10016 Z= 0.127 Angle : 0.621 10.012 13538 Z= 0.314 Chirality : 0.042 0.239 1512 Planarity : 0.005 0.047 1662 Dihedral : 7.349 59.397 1418 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.42 % Allowed : 12.92 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.23), residues: 1146 helix: -1.13 (0.17), residues: 766 sheet: -2.84 (1.01), residues: 22 loop : -3.05 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 492 TYR 0.015 0.001 TYR A 187 PHE 0.016 0.001 PHE B 615 TRP 0.018 0.002 TRP B 155 HIS 0.002 0.001 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10016) covalent geometry : angle 0.62114 / 0.31 (13538) hydrogen bonds : bond 0.04043 / 2.56 ( 448) hydrogen bonds : angle 3.72727 / 2.57 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 0.393 Fit side-chains REVERT: B 22 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: B 233 ASP cc_start: 0.8733 (t0) cc_final: 0.8354 (t0) REVERT: B 543 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: B 564 ASP cc_start: 0.8365 (p0) cc_final: 0.8069 (t0) REVERT: B 650 MET cc_start: 0.9083 (tmm) cc_final: 0.8776 (tmm) REVERT: A 22 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: A 233 ASP cc_start: 0.8720 (t0) cc_final: 0.8345 (t0) REVERT: A 543 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: A 564 ASP cc_start: 0.8362 (p0) cc_final: 0.7974 (t0) REVERT: A 707 MET cc_start: 0.7624 (mpp) cc_final: 0.7381 (mpp) outliers start: 35 outliers final: 18 residues processed: 110 average time/residue: 0.0665 time to fit residues: 11.5840 Evaluate side-chains 89 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.080249 restraints weight = 23413.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082269 restraints weight = 12470.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.083622 restraints weight = 8313.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.084515 restraints weight = 6382.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.084907 restraints weight = 5371.363| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10016 Z= 0.167 Angle : 0.638 8.831 13538 Z= 0.324 Chirality : 0.043 0.239 1512 Planarity : 0.005 0.047 1662 Dihedral : 7.193 53.759 1418 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.89 % Allowed : 12.92 % Favored : 82.19 % 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 are not related in a simple way. whole: -2.01 (0.24), residues: 1146 helix: -0.46 (0.18), residues: 770 sheet: -3.32 (1.06), residues: 22 loop : -3.03 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 65 TYR 0.024 0.002 TYR B 385 PHE 0.017 0.002 PHE B 615 TRP 0.021 0.002 TRP B 578 HIS 0.004 0.001 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (10016) covalent geometry : angle 0.63761 / 0.32 (13538) hydrogen bonds : bond 0.04061 / 2.58 ( 448) hydrogen bonds : angle 3.68624 / 2.55 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 71 time to evaluate : 0.245 Fit side-chains REVERT: B 22 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: B 147 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8581 (p) REVERT: A 22 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: A 147 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8800 (t) outliers start: 50 outliers final: 30 residues processed: 111 average time/residue: 0.0622 time to fit residues: 11.0005 Evaluate side-chains 101 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 116 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.078153 restraints weight = 23671.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.080137 restraints weight = 12646.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081480 restraints weight = 8469.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.082326 restraints weight = 6497.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.082833 restraints weight = 5486.673| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10016 Z= 0.227 Angle : 0.672 8.980 13538 Z= 0.342 Chirality : 0.045 0.218 1512 Planarity : 0.005 0.053 1662 Dihedral : 7.449 53.753 1418 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.79 % Allowed : 13.21 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.24), residues: 1146 helix: -0.25 (0.19), residues: 770 sheet: -3.50 (1.10), residues: 22 loop : -2.95 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 625 TYR 0.027 0.002 TYR A 385 PHE 0.018 0.002 PHE B 615 TRP 0.022 0.002 TRP B 578 HIS 0.005 0.001 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (10016) covalent geometry : angle 0.67154 / 0.34 (13538) hydrogen bonds : bond 0.04330 / 2.75 ( 448) hydrogen bonds : angle 3.81481 / 2.65 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 69 time to evaluate : 0.281 Fit side-chains REVERT: B 22 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: B 147 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8778 (t) REVERT: A 22 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: A 147 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8708 (p) outliers start: 49 outliers final: 35 residues processed: 109 average time/residue: 0.0685 time to fit residues: 11.9263 Evaluate side-chains 103 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 0.1980 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 95 optimal weight: 0.0060 chunk 115 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.080744 restraints weight = 23279.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.082791 restraints weight = 12410.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.084140 restraints weight = 8293.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.085020 restraints weight = 6372.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.085531 restraints weight = 5379.354| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10016 Z= 0.114 Angle : 0.581 7.356 13538 Z= 0.292 Chirality : 0.041 0.224 1512 Planarity : 0.004 0.053 1662 Dihedral : 6.635 51.089 1418 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.01 % Allowed : 14.68 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.25), residues: 1146 helix: 0.19 (0.19), residues: 770 sheet: -3.61 (1.10), residues: 22 loop : -2.66 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.020 0.001 TYR A 385 PHE 0.017 0.001 PHE A 307 TRP 0.011 0.001 TRP B 155 HIS 0.002 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (10016) covalent geometry : angle 0.58065 / 0.29 (13538) hydrogen bonds : bond 0.03405 / 2.16 ( 448) hydrogen bonds : angle 3.40889 / 2.38 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 0.374 Fit side-chains REVERT: B 22 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: B 39 LEU cc_start: 0.9365 (tp) cc_final: 0.9120 (mt) REVERT: B 147 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8678 (t) REVERT: A 22 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: A 147 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8767 (t) outliers start: 41 outliers final: 26 residues processed: 111 average time/residue: 0.0706 time to fit residues: 12.4219 Evaluate side-chains 96 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.080056 restraints weight = 23184.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082102 restraints weight = 12337.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.083441 restraints weight = 8193.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.084328 restraints weight = 6262.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.084854 restraints weight = 5262.682| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10016 Z= 0.138 Angle : 0.597 7.250 13538 Z= 0.301 Chirality : 0.042 0.228 1512 Planarity : 0.004 0.052 1662 Dihedral : 6.483 52.970 1418 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.21 % Allowed : 15.56 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.26), residues: 1146 helix: 0.35 (0.19), residues: 772 sheet: -3.63 (1.08), residues: 22 loop : -2.50 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 492 TYR 0.023 0.001 TYR A 385 PHE 0.016 0.001 PHE B 615 TRP 0.013 0.001 TRP B 578 HIS 0.003 0.001 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (10016) covalent geometry : angle 0.59714 / 0.30 (13538) hydrogen bonds : bond 0.03568 / 2.26 ( 448) hydrogen bonds : angle 3.44707 / 2.40 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 71 time to evaluate : 0.342 Fit side-chains REVERT: B 22 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: B 39 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9129 (mt) REVERT: B 147 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8755 (p) REVERT: A 22 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: A 147 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8603 (p) outliers start: 43 outliers final: 29 residues processed: 108 average time/residue: 0.0610 time to fit residues: 10.5071 Evaluate side-chains 99 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.0670 chunk 98 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.080655 restraints weight = 23170.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.082730 restraints weight = 12331.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.084092 restraints weight = 8157.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.084939 restraints weight = 6229.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.085492 restraints weight = 5265.431| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10016 Z= 0.122 Angle : 0.588 7.621 13538 Z= 0.296 Chirality : 0.042 0.226 1512 Planarity : 0.004 0.053 1662 Dihedral : 6.240 50.726 1418 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.50 % Allowed : 15.85 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.26), residues: 1146 helix: 0.59 (0.19), residues: 766 sheet: -3.58 (1.07), residues: 22 loop : -2.32 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.021 0.001 TYR A 385 PHE 0.019 0.001 PHE A 307 TRP 0.011 0.001 TRP B 84 HIS 0.002 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (10016) covalent geometry : angle 0.58805 / 0.30 (13538) hydrogen bonds : bond 0.03381 / 2.14 ( 448) hydrogen bonds : angle 3.36568 / 2.35 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 64 time to evaluate : 0.318 Fit side-chains REVERT: B 22 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: B 147 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8789 (p) REVERT: A 22 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: A 147 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8643 (p) REVERT: A 707 MET cc_start: 0.7000 (mpp) cc_final: 0.6767 (mpp) outliers start: 46 outliers final: 32 residues processed: 105 average time/residue: 0.0716 time to fit residues: 11.7775 Evaluate side-chains 100 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 64 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.079959 restraints weight = 23192.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.081991 restraints weight = 12395.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.083319 restraints weight = 8286.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084212 restraints weight = 6375.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.084717 restraints weight = 5374.419| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10016 Z= 0.137 Angle : 0.607 7.248 13538 Z= 0.308 Chirality : 0.042 0.227 1512 Planarity : 0.004 0.053 1662 Dihedral : 6.183 51.517 1418 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.21 % Allowed : 16.05 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.26), residues: 1146 helix: 0.70 (0.19), residues: 766 sheet: -3.62 (1.07), residues: 22 loop : -2.29 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 65 TYR 0.022 0.001 TYR A 385 PHE 0.017 0.001 PHE B 615 TRP 0.012 0.001 TRP B 578 HIS 0.003 0.001 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10016) covalent geometry : angle 0.60702 / 0.31 (13538) hydrogen bonds : bond 0.03474 / 2.20 ( 448) hydrogen bonds : angle 3.38174 / 2.36 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 69 time to evaluate : 0.407 Fit side-chains REVERT: B 22 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: B 147 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8816 (t) REVERT: A 22 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: A 39 LEU cc_start: 0.9309 (mt) cc_final: 0.9013 (mt) REVERT: A 147 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8807 (t) REVERT: A 707 MET cc_start: 0.7141 (mpp) cc_final: 0.6879 (mpp) outliers start: 43 outliers final: 36 residues processed: 108 average time/residue: 0.0712 time to fit residues: 11.8975 Evaluate side-chains 102 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 62 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.081902 restraints weight = 22955.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083985 restraints weight = 12142.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.085370 restraints weight = 8040.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.086201 restraints weight = 6137.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.086618 restraints weight = 5183.266| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10016 Z= 0.108 Angle : 0.587 7.365 13538 Z= 0.296 Chirality : 0.041 0.223 1512 Planarity : 0.004 0.051 1662 Dihedral : 5.767 49.412 1418 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.91 % Allowed : 16.73 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.26), residues: 1146 helix: 0.85 (0.20), residues: 772 sheet: -3.51 (1.07), residues: 22 loop : -2.27 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.018 0.001 TYR A 385 PHE 0.016 0.001 PHE B 615 TRP 0.008 0.001 TRP B 84 HIS 0.002 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10016) covalent geometry : angle 0.58696 / 0.30 (13538) hydrogen bonds : bond 0.03127 / 1.98 ( 448) hydrogen bonds : angle 3.22458 / 2.26 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 73 time to evaluate : 0.320 Fit side-chains REVERT: B 22 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: B 147 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8779 (p) REVERT: A 22 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7069 (m-80) REVERT: A 39 LEU cc_start: 0.9303 (mt) cc_final: 0.9003 (mt) REVERT: A 147 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8674 (p) REVERT: A 510 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7423 (m-30) outliers start: 40 outliers final: 32 residues processed: 109 average time/residue: 0.0740 time to fit residues: 12.4307 Evaluate side-chains 101 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 64 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 117 optimal weight: 9.9990 chunk 115 optimal weight: 0.3980 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.097243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082411 restraints weight = 23003.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084503 restraints weight = 12028.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.085880 restraints weight = 7892.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.086731 restraints weight = 6001.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087273 restraints weight = 5061.829| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10016 Z= 0.107 Angle : 0.587 7.569 13538 Z= 0.295 Chirality : 0.041 0.226 1512 Planarity : 0.004 0.049 1662 Dihedral : 5.553 46.886 1418 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.91 % Allowed : 17.03 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1146 helix: 0.98 (0.20), residues: 772 sheet: -3.44 (1.07), residues: 22 loop : -2.26 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.018 0.001 TYR A 385 PHE 0.015 0.001 PHE A 615 TRP 0.009 0.001 TRP B 84 HIS 0.001 0.000 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (10016) covalent geometry : angle 0.58653 / 0.30 (13538) hydrogen bonds : bond 0.03055 / 1.93 ( 448) hydrogen bonds : angle 3.19712 / 2.24 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1218.64 seconds wall clock time: 21 minutes 47.89 seconds (1307.89 seconds total)