Starting phenix.real_space_refine on Fri Feb 14 10:16:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e1o_8959/02_2025/6e1o_8959.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e1o_8959/02_2025/6e1o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6e1o_8959/02_2025/6e1o_8959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e1o_8959/02_2025/6e1o_8959.map" model { file = "/net/cci-nas-00/data/ceres_data/6e1o_8959/02_2025/6e1o_8959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e1o_8959/02_2025/6e1o_8959.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} 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, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} 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: 5.86, per 1000 atoms: 0.60 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: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.22 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: 3.11 Time building geometry restraints manager: 2.73 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.770 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 23.590 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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= 0.516 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 : 4.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.051 0.004 TRP A 578 HIS 0.007 0.003 HIS A 15 PHE 0.030 0.003 PHE B 208 TYR 0.036 0.003 TYR A 385 ARG 0.006 0.001 ARG B 557 *********************** 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 : 1.537 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: 0.7120 (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: 0.9253 (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: 0.6967 (m) REVERT: B 616 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: B 618 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8675 (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: 0.7095 (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: 0.9254 (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: 0.8673 (tm-30) REVERT: A 639 ASN cc_start: 0.8867 (m110) cc_final: 0.8566 (m-40) outliers start: 8 outliers final: 1 residues processed: 210 average time/residue: 0.2644 time to fit residues: 73.6133 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 : 1.049 ------------------------------------------------------------------------------- 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 99 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 150 GLN B 280 GLN A 148 ASN A 150 GLN A 280 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.098933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.084073 restraints weight = 22971.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.086221 restraints weight = 12127.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.087551 restraints weight = 8010.281| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10016 Z= 0.196 Angle : 0.698 11.686 13538 Z= 0.355 Chirality : 0.043 0.266 1512 Planarity : 0.006 0.058 1662 Dihedral : 8.164 58.507 1422 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.03 % Allowed : 11.25 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.20), residues: 1146 helix: -2.29 (0.15), residues: 764 sheet: -3.09 (0.96), residues: 22 loop : -3.15 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 578 HIS 0.002 0.001 HIS A 176 PHE 0.018 0.002 PHE A 160 TYR 0.014 0.002 TYR A 187 ARG 0.005 0.001 ARG B 644 *********************** 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 134 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 1.054 Fit side-chains REVERT: B 22 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: B 233 ASP cc_start: 0.8628 (t0) cc_final: 0.8379 (t0) REVERT: B 564 ASP cc_start: 0.8282 (p0) cc_final: 0.8039 (t0) REVERT: A 233 ASP cc_start: 0.8578 (t0) cc_final: 0.8319 (t0) REVERT: A 564 ASP cc_start: 0.8280 (p0) cc_final: 0.7972 (t0) REVERT: A 650 MET cc_start: 0.9052 (tmm) cc_final: 0.8818 (tmm) REVERT: A 707 MET cc_start: 0.7588 (mpp) cc_final: 0.7333 (mpp) outliers start: 31 outliers final: 10 residues processed: 133 average time/residue: 0.1677 time to fit residues: 34.4554 Evaluate side-chains 83 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 54 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN B 247 HIS A 230 GLN A 247 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.081495 restraints weight = 23210.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.083578 restraints weight = 12366.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.084958 restraints weight = 8220.839| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10016 Z= 0.218 Angle : 0.640 9.794 13538 Z= 0.326 Chirality : 0.043 0.249 1512 Planarity : 0.005 0.046 1662 Dihedral : 7.387 57.349 1418 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.82 % Allowed : 13.21 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.23), residues: 1146 helix: -1.10 (0.17), residues: 768 sheet: -2.75 (1.05), residues: 22 loop : -3.08 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 155 HIS 0.003 0.001 HIS B 15 PHE 0.018 0.001 PHE B 615 TYR 0.024 0.002 TYR A 385 ARG 0.004 0.000 ARG A 492 *********************** 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 115 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 76 time to evaluate : 1.094 Fit side-chains REVERT: B 22 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: A 650 MET cc_start: 0.9145 (tmm) cc_final: 0.8945 (tmm) outliers start: 39 outliers final: 22 residues processed: 104 average time/residue: 0.1866 time to fit residues: 30.3626 Evaluate side-chains 88 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain B residue 281 LEU 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 19 VAL 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 516 CYS 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 32 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 0.0010 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 7 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 overall best weight: 1.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS A 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.081858 restraints weight = 23037.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.083900 restraints weight = 12244.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.085262 restraints weight = 8135.449| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3865 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= 0.199 Angle : 0.608 9.090 13538 Z= 0.306 Chirality : 0.042 0.230 1512 Planarity : 0.004 0.046 1662 Dihedral : 7.017 56.216 1418 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.60 % Allowed : 13.31 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.24), residues: 1146 helix: -0.45 (0.18), residues: 772 sheet: -2.99 (1.06), residues: 22 loop : -3.01 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 578 HIS 0.002 0.001 HIS B 15 PHE 0.016 0.001 PHE B 615 TYR 0.020 0.001 TYR A 385 ARG 0.004 0.000 ARG B 492 *********************** 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 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 79 time to evaluate : 0.884 Fit side-chains REVERT: B 22 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: B 33 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7871 (pt) REVERT: B 169 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9071 (tt) REVERT: A 147 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8794 (t) outliers start: 47 outliers final: 26 residues processed: 116 average time/residue: 0.1617 time to fit residues: 29.3216 Evaluate side-chains 100 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 33 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 169 ILE 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 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 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 305 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 493 PHE 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 4 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 48 optimal weight: 0.0370 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.097193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082211 restraints weight = 22910.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.084296 restraints weight = 12201.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.085651 restraints weight = 8109.377| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10016 Z= 0.173 Angle : 0.585 7.298 13538 Z= 0.294 Chirality : 0.041 0.226 1512 Planarity : 0.004 0.042 1662 Dihedral : 6.734 57.399 1418 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.52 % Allowed : 14.58 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.25), residues: 1146 helix: 0.01 (0.19), residues: 772 sheet: -3.04 (1.08), residues: 22 loop : -2.78 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 578 HIS 0.002 0.001 HIS B 619 PHE 0.016 0.001 PHE B 615 TYR 0.020 0.001 TYR A 385 ARG 0.003 0.000 ARG B 492 *********************** 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 122 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 1.086 Fit side-chains REVERT: B 22 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: B 169 ILE cc_start: 0.9312 (mt) cc_final: 0.9108 (tt) REVERT: A 147 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8839 (t) outliers start: 36 outliers final: 26 residues processed: 116 average time/residue: 0.1730 time to fit residues: 30.8471 Evaluate side-chains 97 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain B residue 281 LEU 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 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 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 281 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 493 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 65 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 111 optimal weight: 0.0870 chunk 112 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.078973 restraints weight = 23161.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.080976 restraints weight = 12402.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.082300 restraints weight = 8303.246| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10016 Z= 0.285 Angle : 0.636 7.310 13538 Z= 0.324 Chirality : 0.044 0.227 1512 Planarity : 0.005 0.044 1662 Dihedral : 6.984 56.601 1418 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.60 % Allowed : 14.97 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1146 helix: 0.22 (0.19), residues: 766 sheet: -3.20 (1.10), residues: 22 loop : -2.66 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 578 HIS 0.004 0.001 HIS B 15 PHE 0.017 0.002 PHE B 615 TYR 0.026 0.002 TYR A 385 ARG 0.003 0.001 ARG B 557 *********************** 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 117 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 70 time to evaluate : 1.068 Fit side-chains REVERT: B 22 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: B 159 THR cc_start: 0.8546 (p) cc_final: 0.8227 (t) outliers start: 47 outliers final: 26 residues processed: 108 average time/residue: 0.1664 time to fit residues: 28.1744 Evaluate side-chains 92 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 281 LEU Chi-restraints excluded: chain B residue 305 GLU 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 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 281 LEU Chi-restraints excluded: chain A residue 305 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.096618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.081562 restraints weight = 23300.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083660 restraints weight = 12270.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.085057 restraints weight = 8126.191| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4399 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= 0.159 Angle : 0.578 7.153 13538 Z= 0.291 Chirality : 0.041 0.229 1512 Planarity : 0.004 0.043 1662 Dihedral : 6.467 57.901 1418 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.72 % Allowed : 15.66 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.26), residues: 1146 helix: 0.48 (0.19), residues: 770 sheet: -3.13 (1.06), residues: 22 loop : -2.58 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 578 HIS 0.002 0.000 HIS B 619 PHE 0.017 0.001 PHE B 307 TYR 0.019 0.001 TYR A 385 ARG 0.003 0.000 ARG A 65 *********************** 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 112 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 1.084 Fit side-chains REVERT: B 22 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: B 39 LEU cc_start: 0.9347 (mt) cc_final: 0.9065 (mt) REVERT: B 159 THR cc_start: 0.8514 (p) cc_final: 0.8226 (t) REVERT: A 39 LEU cc_start: 0.9290 (mt) cc_final: 0.9010 (mt) outliers start: 38 outliers final: 32 residues processed: 106 average time/residue: 0.1690 time to fit residues: 27.9381 Evaluate side-chains 100 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 160 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 LEU 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 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 LEU 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 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 47 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 103 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.081292 restraints weight = 23330.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.083387 restraints weight = 12360.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.084751 restraints weight = 8196.059| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4487 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= 0.177 Angle : 0.581 7.397 13538 Z= 0.293 Chirality : 0.041 0.232 1512 Planarity : 0.004 0.043 1662 Dihedral : 6.353 58.624 1418 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.11 % Allowed : 15.95 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.26), residues: 1146 helix: 0.67 (0.19), residues: 772 sheet: -3.22 (1.02), residues: 22 loop : -2.44 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 578 HIS 0.002 0.001 HIS B 15 PHE 0.018 0.001 PHE A 307 TYR 0.020 0.001 TYR B 385 ARG 0.003 0.000 ARG A 65 *********************** 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 109 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 67 time to evaluate : 1.169 Fit side-chains REVERT: B 22 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: B 39 LEU cc_start: 0.9301 (mt) cc_final: 0.9024 (mt) REVERT: B 159 THR cc_start: 0.8518 (p) cc_final: 0.8234 (t) outliers start: 42 outliers final: 35 residues processed: 103 average time/residue: 0.1756 time to fit residues: 28.1025 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 : 1.121 ------------------------------------------------------------------------------- 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 160 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 LEU 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 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 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 61 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 57 optimal weight: 0.0770 chunk 97 optimal weight: 7.9990 chunk 55 optimal weight: 0.0870 chunk 84 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.098327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.083291 restraints weight = 22972.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.085399 restraints weight = 12162.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.086774 restraints weight = 8055.654| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10016 Z= 0.143 Angle : 0.575 7.698 13538 Z= 0.289 Chirality : 0.040 0.227 1512 Planarity : 0.004 0.040 1662 Dihedral : 6.016 59.424 1418 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.33 % Allowed : 16.63 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1146 helix: 0.93 (0.20), residues: 770 sheet: -3.23 (1.02), residues: 22 loop : -2.24 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 84 HIS 0.001 0.000 HIS A 619 PHE 0.017 0.001 PHE A 160 TYR 0.016 0.001 TYR A 385 ARG 0.002 0.000 ARG B 492 *********************** 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 113 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 1.107 Fit side-chains REVERT: B 22 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7301 (m-80) REVERT: B 159 THR cc_start: 0.8469 (p) cc_final: 0.8195 (t) REVERT: B 707 MET cc_start: 0.7352 (mmm) cc_final: 0.6993 (mmm) REVERT: A 39 LEU cc_start: 0.9303 (mt) cc_final: 0.8998 (mt) outliers start: 34 outliers final: 29 residues processed: 109 average time/residue: 0.2128 time to fit residues: 33.9403 Evaluate side-chains 100 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 LEU 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 518 GLN 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 211 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 LEU 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 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 95 optimal weight: 0.7980 chunk 67 optimal weight: 0.0570 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083119 restraints weight = 23186.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.085240 restraints weight = 12211.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.086623 restraints weight = 8057.144| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10016 Z= 0.158 Angle : 0.593 8.919 13538 Z= 0.299 Chirality : 0.040 0.231 1512 Planarity : 0.004 0.040 1662 Dihedral : 5.821 58.939 1418 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.13 % Allowed : 17.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1146 helix: 1.01 (0.20), residues: 772 sheet: -3.24 (1.01), residues: 22 loop : -2.17 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 84 HIS 0.002 0.001 HIS A 143 PHE 0.016 0.001 PHE A 160 TYR 0.017 0.001 TYR A 385 ARG 0.005 0.000 ARG B 279 ********************** 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 102 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 1.172 Fit side-chains REVERT: B 22 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.7288 (m-80) REVERT: B 39 LEU cc_start: 0.9290 (mt) cc_final: 0.8996 (mt) REVERT: B 159 THR cc_start: 0.8463 (p) cc_final: 0.8200 (t) REVERT: B 707 MET cc_start: 0.6606 (mmm) cc_final: 0.5217 (mmt) outliers start: 32 outliers final: 28 residues processed: 97 average time/residue: 0.1892 time to fit residues: 27.8027 Evaluate side-chains 94 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 282 LEU 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 518 GLN Chi-restraints excluded: chain B residue 590 MET 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 211 ILE Chi-restraints excluded: chain A residue 282 LEU 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 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 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 100 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083157 restraints weight = 23030.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.085291 restraints weight = 12056.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.086659 restraints weight = 7909.621| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10016 Z= 0.155 Angle : 0.589 8.040 13538 Z= 0.297 Chirality : 0.040 0.230 1512 Planarity : 0.004 0.041 1662 Dihedral : 5.700 58.638 1418 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.03 % Allowed : 17.42 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1146 helix: 0.98 (0.20), residues: 784 sheet: -3.19 (1.03), residues: 22 loop : -2.01 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 706 HIS 0.002 0.000 HIS A 143 PHE 0.016 0.001 PHE A 160 TYR 0.017 0.001 TYR A 385 ARG 0.007 0.000 ARG B 708 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2426.87 seconds wall clock time: 44 minutes 38.83 seconds (2678.83 seconds total)