Starting phenix.real_space_refine on Mon Jul 28 05:58:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e1o_8959/07_2025/6e1o_8959.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e1o_8959/07_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_8959/07_2025/6e1o_8959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e1o_8959/07_2025/6e1o_8959.map" model { file = "/net/cci-nas-00/data/ceres_data/6e1o_8959/07_2025/6e1o_8959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e1o_8959/07_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-5711/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: 6.74, per 1000 atoms: 0.69 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: 2.55 Conformation dependent library (CDL) restraints added in 1.2 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: 0.89 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: 2.41 Time building geometry restraints manager: 2.93 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: 0.960 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.410 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.150 ------------------------------------------------------------------------------- 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= 0.358 Angle : 1.210 9.928 13538 Z= 0.609 Chirality : 0.063 0.266 1512 Planarity : 0.008 0.075 1662 Dihedral : 11.661 71.647 3642 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.62 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 Details of bonding type rmsd hydrogen bonds : bond 0.31465 ( 448) hydrogen bonds : angle 10.46344 ( 1332) covalent geometry : bond 0.00815 (10016) covalent geometry : angle 1.20996 (13538) *********************** 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 : 1.061 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: 0.2697 time to fit residues: 75.0464 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 : 1.186 ------------------------------------------------------------------------------- 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 = 0.098961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.084066 restraints weight = 22961.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.086197 restraints weight = 12141.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087600 restraints weight = 8043.200| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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= 0.139 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 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 448) hydrogen bonds : angle 4.32947 ( 1332) covalent geometry : bond 0.00309 (10016) covalent geometry : angle 0.69813 (13538) *********************** 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 : 1.161 Fit side-chains REVERT: B 22 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: B 233 ASP cc_start: 0.8621 (t0) cc_final: 0.8373 (t0) REVERT: B 564 ASP cc_start: 0.8276 (p0) cc_final: 0.8040 (t0) REVERT: A 233 ASP cc_start: 0.8572 (t0) cc_final: 0.8313 (t0) REVERT: A 564 ASP cc_start: 0.8278 (p0) cc_final: 0.7975 (t0) REVERT: A 650 MET cc_start: 0.9050 (tmm) cc_final: 0.8818 (tmm) REVERT: A 707 MET cc_start: 0.7585 (mpp) cc_final: 0.7326 (mpp) outliers start: 31 outliers final: 10 residues processed: 133 average time/residue: 0.1674 time to fit residues: 34.4886 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 : 1.089 ------------------------------------------------------------------------------- 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: 3.9990 chunk 80 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 8 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.096199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.081314 restraints weight = 23223.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083383 restraints weight = 12358.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084767 restraints weight = 8222.218| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10016 Z= 0.157 Angle : 0.647 10.052 13538 Z= 0.329 Chirality : 0.043 0.246 1512 Planarity : 0.005 0.047 1662 Dihedral : 7.464 57.428 1418 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.91 % Allowed : 13.11 % 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: -2.74 (0.23), residues: 1146 helix: -1.13 (0.17), residues: 768 sheet: -2.67 (1.06), residues: 22 loop : -3.09 (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 0.018 0.002 TYR A 385 ARG 0.004 0.000 ARG A 492 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 448) hydrogen bonds : angle 3.80287 ( 1332) covalent geometry : bond 0.00365 (10016) covalent geometry : angle 0.64687 (13538) *********************** 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 116 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 1.093 Fit side-chains REVERT: B 22 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: A 650 MET cc_start: 0.9135 (tmm) cc_final: 0.8930 (tmm) outliers start: 40 outliers final: 24 residues processed: 106 average time/residue: 0.1633 time to fit residues: 27.1601 Evaluate side-chains 88 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.092565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.077808 restraints weight = 23488.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.079804 restraints weight = 12644.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.081148 restraints weight = 8437.506| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10016 Z= 0.245 Angle : 0.710 9.629 13538 Z= 0.363 Chirality : 0.047 0.228 1512 Planarity : 0.005 0.056 1662 Dihedral : 7.960 59.753 1418 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.68 % Allowed : 12.62 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.23), residues: 1146 helix: -0.69 (0.18), residues: 770 sheet: -3.13 (1.06), residues: 22 loop : -3.15 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 578 HIS 0.006 0.001 HIS A 15 PHE 0.018 0.002 PHE B 615 TYR 0.026 0.002 TYR B 385 ARG 0.004 0.001 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.04643 ( 448) hydrogen bonds : angle 3.97325 ( 1332) covalent geometry : bond 0.00581 (10016) covalent geometry : angle 0.71011 (13538) *********************** 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 132 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 74 time to evaluate : 1.092 Fit side-chains REVERT: B 22 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: B 147 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8512 (p) REVERT: A 147 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8846 (t) REVERT: A 650 MET cc_start: 0.9171 (tmm) cc_final: 0.8959 (tmm) REVERT: A 707 MET cc_start: 0.7513 (mpp) cc_final: 0.7174 (mpp) outliers start: 58 outliers final: 38 residues processed: 119 average time/residue: 0.1651 time to fit residues: 30.7185 Evaluate side-chains 107 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 66 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 555 CYS 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 39 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 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 532 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 4 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.094080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.079272 restraints weight = 23126.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.081291 restraints weight = 12315.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082652 restraints weight = 8202.881| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10016 Z= 0.153 Angle : 0.626 9.355 13538 Z= 0.317 Chirality : 0.043 0.227 1512 Planarity : 0.005 0.055 1662 Dihedral : 7.447 58.575 1418 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.70 % Allowed : 14.09 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.25), residues: 1146 helix: -0.23 (0.19), residues: 770 sheet: -3.14 (1.08), residues: 22 loop : -2.94 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 155 HIS 0.003 0.001 HIS A 15 PHE 0.017 0.002 PHE B 615 TYR 0.024 0.001 TYR A 385 ARG 0.003 0.000 ARG A 492 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 448) hydrogen bonds : angle 3.64668 ( 1332) covalent geometry : bond 0.00364 (10016) covalent geometry : angle 0.62553 (13538) *********************** 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 120 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 72 time to evaluate : 0.987 Fit side-chains REVERT: B 22 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: B 147 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8604 (p) REVERT: A 147 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8668 (p) REVERT: A 650 MET cc_start: 0.9166 (tmm) cc_final: 0.8935 (tmm) REVERT: A 707 MET cc_start: 0.7417 (mpp) cc_final: 0.7162 (mpp) outliers start: 48 outliers final: 34 residues processed: 113 average time/residue: 0.1979 time to fit residues: 35.3372 Evaluate side-chains 100 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 292 VAL 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 535 SER Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 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 535 SER Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 65 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.092388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077660 restraints weight = 23185.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.079653 restraints weight = 12401.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.080979 restraints weight = 8277.416| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10016 Z= 0.208 Angle : 0.648 7.405 13538 Z= 0.331 Chirality : 0.045 0.226 1512 Planarity : 0.005 0.057 1662 Dihedral : 7.334 55.048 1418 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.48 % Allowed : 14.09 % 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: -1.50 (0.25), residues: 1146 helix: -0.08 (0.19), residues: 766 sheet: -3.28 (1.04), residues: 22 loop : -2.77 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 155 HIS 0.005 0.001 HIS A 15 PHE 0.017 0.002 PHE B 615 TYR 0.028 0.002 TYR B 385 ARG 0.003 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 448) hydrogen bonds : angle 3.79275 ( 1332) covalent geometry : bond 0.00496 (10016) covalent geometry : angle 0.64757 (13538) *********************** 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 121 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 65 time to evaluate : 1.232 Fit side-chains REVERT: B 22 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: B 147 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8658 (p) REVERT: A 147 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8767 (t) REVERT: A 650 MET cc_start: 0.9207 (tmm) cc_final: 0.8955 (tmm) outliers start: 56 outliers final: 41 residues processed: 114 average time/residue: 0.1660 time to fit residues: 29.6357 Evaluate side-chains 109 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 65 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 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 385 TYR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 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 281 LEU Chi-restraints excluded: chain A residue 292 VAL 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 508 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 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: 1.9990 chunk 31 optimal weight: 6.9990 chunk 95 optimal weight: 0.2980 chunk 57 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.095361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.080446 restraints weight = 23313.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.082535 restraints weight = 12340.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.083891 restraints weight = 8137.882| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4443 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= 0.113 Angle : 0.585 8.038 13538 Z= 0.294 Chirality : 0.041 0.221 1512 Planarity : 0.004 0.055 1662 Dihedral : 6.687 55.922 1418 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.70 % Allowed : 14.97 % Favored : 80.33 % 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: -1.05 (0.25), residues: 1146 helix: 0.25 (0.19), residues: 770 sheet: -3.21 (1.03), residues: 22 loop : -2.62 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 155 HIS 0.002 0.001 HIS B 619 PHE 0.018 0.001 PHE A 307 TYR 0.020 0.001 TYR A 385 ARG 0.002 0.000 ARG B 492 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 448) hydrogen bonds : angle 3.38840 ( 1332) covalent geometry : bond 0.00259 (10016) covalent geometry : angle 0.58492 (13538) *********************** 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 127 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 79 time to evaluate : 1.090 Fit side-chains REVERT: B 22 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: B 39 LEU cc_start: 0.9311 (mt) cc_final: 0.9046 (mt) REVERT: B 147 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8670 (t) REVERT: A 147 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8568 (p) REVERT: A 650 MET cc_start: 0.9146 (tmm) cc_final: 0.8932 (tmm) outliers start: 48 outliers final: 39 residues processed: 119 average time/residue: 0.1651 time to fit residues: 30.6876 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 : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 185 GLN 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 398 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 24 TYR 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 281 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 532 VAL 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: 0.6980 chunk 49 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.095399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.080562 restraints weight = 23338.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.082633 restraints weight = 12263.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083999 restraints weight = 8091.156| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4518 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= 0.116 Angle : 0.596 9.964 13538 Z= 0.296 Chirality : 0.042 0.226 1512 Planarity : 0.004 0.054 1662 Dihedral : 6.557 57.733 1418 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.40 % Allowed : 16.24 % 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: -0.74 (0.26), residues: 1146 helix: 0.48 (0.19), residues: 770 sheet: -3.25 (1.00), residues: 22 loop : -2.45 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 84 HIS 0.002 0.001 HIS B 15 PHE 0.016 0.001 PHE B 615 TYR 0.021 0.001 TYR A 385 ARG 0.003 0.000 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 448) hydrogen bonds : angle 3.31101 ( 1332) covalent geometry : bond 0.00270 (10016) covalent geometry : angle 0.59613 (13538) *********************** 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 116 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 71 time to evaluate : 1.142 Fit side-chains REVERT: B 22 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: B 147 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 147 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8702 (p) REVERT: A 650 MET cc_start: 0.9161 (tmm) cc_final: 0.8920 (tmm) outliers start: 45 outliers final: 37 residues processed: 111 average time/residue: 0.1669 time to fit residues: 28.7867 Evaluate side-chains 105 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 65 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 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 386 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 532 VAL 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: 3.9990 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 57 optimal weight: 0.0870 chunk 97 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 overall best weight: 1.3962 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.094625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.079811 restraints weight = 23213.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.081843 restraints weight = 12358.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083183 restraints weight = 8196.020| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4544 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= 0.132 Angle : 0.614 9.548 13538 Z= 0.307 Chirality : 0.042 0.228 1512 Planarity : 0.004 0.054 1662 Dihedral : 6.488 57.275 1418 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.40 % Allowed : 16.05 % 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: -0.53 (0.26), residues: 1146 helix: 0.63 (0.20), residues: 766 sheet: -3.26 (1.00), residues: 22 loop : -2.31 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 84 HIS 0.002 0.001 HIS B 15 PHE 0.020 0.001 PHE A 307 TYR 0.023 0.001 TYR A 385 ARG 0.002 0.000 ARG B 492 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 448) hydrogen bonds : angle 3.33876 ( 1332) covalent geometry : bond 0.00311 (10016) covalent geometry : angle 0.61378 (13538) *********************** 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 114 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 69 time to evaluate : 1.235 Fit side-chains REVERT: B 22 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: B 39 LEU cc_start: 0.9308 (mt) cc_final: 0.9013 (mt) REVERT: B 147 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8696 (p) REVERT: A 39 LEU cc_start: 0.9308 (mt) cc_final: 0.8989 (mt) REVERT: A 147 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8613 (p) REVERT: A 650 MET cc_start: 0.9198 (tmm) cc_final: 0.8948 (tmm) outliers start: 45 outliers final: 41 residues processed: 108 average time/residue: 0.1760 time to fit residues: 29.6191 Evaluate side-chains 111 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 67 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 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 508 VAL Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 646 GLU 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 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 393 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 532 VAL 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: 2.9990 chunk 67 optimal weight: 0.0270 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 23 optimal weight: 0.0470 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 overall best weight: 1.1940 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.095300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.080390 restraints weight = 23365.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.082442 restraints weight = 12390.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.083811 restraints weight = 8213.109| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4593 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= 0.123 Angle : 0.612 9.439 13538 Z= 0.305 Chirality : 0.042 0.228 1512 Planarity : 0.004 0.054 1662 Dihedral : 6.377 57.755 1418 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.50 % Allowed : 16.34 % Favored : 79.16 % 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: -0.41 (0.26), residues: 1146 helix: 0.63 (0.19), residues: 780 sheet: -3.27 (0.99), residues: 22 loop : -2.10 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 84 HIS 0.002 0.001 HIS B 619 PHE 0.017 0.001 PHE A 307 TYR 0.022 0.001 TYR B 385 ARG 0.005 0.000 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 448) hydrogen bonds : angle 3.29006 ( 1332) covalent geometry : bond 0.00287 (10016) covalent geometry : angle 0.61239 (13538) ********************** 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 117 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 71 time to evaluate : 1.067 Fit side-chains REVERT: B 39 LEU cc_start: 0.9298 (mt) cc_final: 0.8987 (mt) REVERT: B 147 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8742 (p) REVERT: A 39 LEU cc_start: 0.9305 (mt) cc_final: 0.8983 (mt) REVERT: A 147 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8698 (p) REVERT: A 650 MET cc_start: 0.9164 (tmm) cc_final: 0.8920 (tmm) REVERT: A 707 MET cc_start: 0.7186 (mpp) cc_final: 0.6898 (mpp) outliers start: 46 outliers final: 41 residues processed: 112 average time/residue: 0.1740 time to fit residues: 29.9116 Evaluate side-chains 108 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 65 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 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 508 VAL Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 646 GLU 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 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 393 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 532 VAL 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: 0.8980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN A 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.080996 restraints weight = 23096.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083079 restraints weight = 12235.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.084455 restraints weight = 8079.788| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10016 Z= 0.112 Angle : 0.599 9.418 13538 Z= 0.297 Chirality : 0.041 0.227 1512 Planarity : 0.004 0.053 1662 Dihedral : 6.183 58.889 1418 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.21 % Allowed : 17.03 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1146 helix: 0.74 (0.20), residues: 782 sheet: -3.26 (0.98), residues: 22 loop : -2.08 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 84 HIS 0.002 0.000 HIS B 15 PHE 0.016 0.001 PHE B 307 TYR 0.020 0.001 TYR B 385 ARG 0.003 0.000 ARG B 492 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 448) hydrogen bonds : angle 3.22390 ( 1332) covalent geometry : bond 0.00260 (10016) covalent geometry : angle 0.59943 (13538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2632.28 seconds wall clock time: 46 minutes 45.29 seconds (2805.29 seconds total)