Starting phenix.real_space_refine on Thu Aug 6 17:01:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vos_65226/08_2026/9vos_65226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vos_65226/08_2026/9vos_65226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vos_65226/08_2026/9vos_65226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vos_65226/08_2026/9vos_65226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vos_65226/08_2026/9vos_65226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vos_65226/08_2026/9vos_65226.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 P 2 5.49 5 S 101 5.16 5 C 10387 2.51 5 N 2579 2.21 5 O 2834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15903 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4602 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 26, 'TRANS': 563} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "A" Number of atoms: 4714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4714 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 28, 'TRANS': 576} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 3, 'HIS:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1568 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 9, 'TRANS': 180} Chain breaks: 1 Chain: "D" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2424 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 309} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 336 Unusual residues: {'CLR': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 378 Unusual residues: {'CLR': 10, 'PEE': 1, 'PII': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 3.16, per 1000 atoms: 0.20 Number of scatterers: 15903 At special positions: 0 Unit cell: (188.568, 207.774, 130.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 2 15.00 O 2834 8.00 N 2579 7.00 C 10387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 272 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 354 " distance=2.05 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 352 " distance=2.05 Simple disulfide: pdb=" SG CYS B 337 " - pdb=" SG CYS B 392 " distance=2.05 Simple disulfide: pdb=" SG CYS B 395 " - pdb=" SG CYS B 402 " distance=2.03 Simple disulfide: pdb=" SG CYS B 481 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 354 " distance=2.04 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 352 " distance=2.04 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 402 " distance=2.03 Simple disulfide: pdb=" SG CYS A 481 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 617.0 milliseconds 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 17 sheets defined 36.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 66 through 74 removed outlier: 3.599A pdb=" N LEU B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 removed outlier: 3.596A pdb=" N TYR B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.840A pdb=" N SER B 91 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 142 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 164 removed outlier: 3.703A pdb=" N TYR B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 292 through 297 removed outlier: 4.515A pdb=" N LEU B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 416 through 442 removed outlier: 3.616A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 432 " --> pdb=" O MET B 428 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 451 removed outlier: 3.799A pdb=" N SER B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 471 removed outlier: 4.161A pdb=" N ILE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) Proline residue: B 468 - end of helix Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 491 through 496 Processing helix chain 'B' and resid 498 through 509 removed outlier: 3.904A pdb=" N HIS B 504 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 508 " --> pdb=" O HIS B 504 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 509 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 removed outlier: 3.734A pdb=" N THR B 514 " --> pdb=" O PHE B 510 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 515' Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 535 through 550 removed outlier: 3.812A pdb=" N SER B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 599 removed outlier: 3.675A pdb=" N VAL B 584 " --> pdb=" O TYR B 580 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 591 " --> pdb=" O PHE B 587 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TRP B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 634 removed outlier: 3.551A pdb=" N VAL B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA B 616 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 617 " --> pdb=" O MET B 613 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU B 621 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE B 622 " --> pdb=" O HIS B 618 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 652 removed outlier: 3.787A pdb=" N MET B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 646 " --> pdb=" O TRP B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 662 removed outlier: 3.806A pdb=" N THR B 658 " --> pdb=" O THR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 667 Processing helix chain 'B' and resid 713 through 730 removed outlier: 3.517A pdb=" N LYS B 720 " --> pdb=" O ASP B 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 74 removed outlier: 3.692A pdb=" N LYS A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 90 through 95 removed outlier: 4.189A pdb=" N LYS A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 141 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 166 removed outlier: 4.014A pdb=" N VAL A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.521A pdb=" N TRP A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 442 removed outlier: 4.167A pdb=" N ILE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 464 removed outlier: 3.743A pdb=" N LEU A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 475 removed outlier: 3.903A pdb=" N VAL A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 472 " --> pdb=" O PRO A 468 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 487 removed outlier: 3.627A pdb=" N ARG A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 512 removed outlier: 4.637A pdb=" N THR A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 555 removed outlier: 3.895A pdb=" N ALA A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A 553 " --> pdb=" O CYS A 549 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 582 removed outlier: 4.018A pdb=" N TYR A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 4.112A pdb=" N PHE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 598 removed outlier: 3.996A pdb=" N TYR A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 634 removed outlier: 4.082A pdb=" N ALA A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 616 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 617 " --> pdb=" O MET A 613 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 622 " --> pdb=" O HIS A 618 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 627 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.667A pdb=" N MET A 643 " --> pdb=" O GLN A 639 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 662 removed outlier: 3.812A pdb=" N THR A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 732 removed outlier: 3.814A pdb=" N ASP A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG A 715 " --> pdb=" O PRO A 711 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS A 731 " --> pdb=" O ILE A 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 36 removed outlier: 3.569A pdb=" N ASP C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 3.756A pdb=" N ILE C 62 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 63 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 112 through 120 Proline residue: C 117 - end of helix removed outlier: 3.515A pdb=" N CYS C 120 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 138 removed outlier: 3.722A pdb=" N TYR C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 160 removed outlier: 3.869A pdb=" N GLU C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 180 removed outlier: 3.553A pdb=" N ILE C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 200 removed outlier: 4.034A pdb=" N GLU C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 195 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N PHE C 196 " --> pdb=" O GLN C 192 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS C 200 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 43 Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'H' and resid 66 through 70 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'I' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.992A pdb=" N ILE B 176 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 191 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 285 through 289 removed outlier: 3.864A pdb=" N MET B 304 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 559 through 563 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 176 Processing sheet with id=AA5, first strand: chain 'A' and resid 559 through 563 Processing sheet with id=AA6, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AA7, first strand: chain 'D' and resid 54 through 60 removed outlier: 5.586A pdb=" N THR D 55 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA D 353 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 66 through 71 removed outlier: 6.840A pdb=" N SER D 81 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N MET D 69 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL D 79 " --> pdb=" O MET D 69 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP D 71 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG D 77 " --> pdb=" O TRP D 71 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 78 " --> pdb=" O TRP D 90 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP D 91 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LYS D 97 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 110 through 113 removed outlier: 6.535A pdb=" N CYS D 129 " --> pdb=" O VAL D 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 156 through 161 removed outlier: 7.252A pdb=" N ALA D 171 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N CYS D 159 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU D 169 " --> pdb=" O CYS D 159 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE D 161 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN D 167 " --> pdb=" O PHE D 161 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER D 172 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN D 189 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP D 181 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 187 " --> pdb=" O ASP D 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 198 through 203 removed outlier: 3.749A pdb=" N PHE D 212 " --> pdb=" O TRP D 224 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN D 233 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 242 through 247 removed outlier: 3.617A pdb=" N PHE D 254 " --> pdb=" O TYR D 266 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 286 through 291 removed outlier: 3.632A pdb=" N SER D 288 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER D 319 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP D 311 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG D 317 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 14 removed outlier: 4.309A pdb=" N GLY H 11 " --> pdb=" O GLN H 117 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR H 119 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR H 116 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 22 through 24 removed outlier: 4.136A pdb=" N TYR H 83 " --> pdb=" O SER H 74 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 74 " --> pdb=" O TYR H 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 11 through 13 removed outlier: 4.311A pdb=" N GLY I 11 " --> pdb=" O GLN I 117 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR I 119 " --> pdb=" O GLY I 11 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR I 116 " --> pdb=" O TYR I 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 21 through 24 removed outlier: 3.523A pdb=" N LEU I 21 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL I 82 " --> pdb=" O CYS I 23 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR I 83 " --> pdb=" O SER I 74 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER I 74 " --> pdb=" O TYR I 83 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1251 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: 2.19 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2482 1.32 - 1.45: 4485 1.45 - 1.58: 9202 1.58 - 1.72: 5 1.72 - 1.85: 148 Bond restraints: 16322 Sorted by residual: bond pdb=" CRD PII A 812 " pdb=" CRE PII A 812 " ideal model delta sigma weight residual 1.524 1.338 0.186 2.00e-02 2.50e+03 8.65e+01 bond pdb=" CRA PII A 812 " pdb=" CRB PII A 812 " ideal model delta sigma weight residual 1.523 1.338 0.185 2.00e-02 2.50e+03 8.57e+01 bond pdb=" CR7 PII A 812 " pdb=" CR8 PII A 812 " ideal model delta sigma weight residual 1.524 1.342 0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" N PRO B 79 " pdb=" CA PRO B 79 " ideal model delta sigma weight residual 1.469 1.549 -0.080 1.28e-02 6.10e+03 3.96e+01 bond pdb=" CA LEU B 535 " pdb=" C LEU B 535 " ideal model delta sigma weight residual 1.523 1.447 0.076 1.34e-02 5.57e+03 3.20e+01 ... (remaining 16317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 22117 4.51 - 9.02: 120 9.02 - 13.54: 19 13.54 - 18.05: 7 18.05 - 22.56: 1 Bond angle restraints: 22264 Sorted by residual: angle pdb=" C ALA A 349 " pdb=" N TYR A 350 " pdb=" CA TYR A 350 " ideal model delta sigma weight residual 122.67 100.11 22.56 1.59e+00 3.96e-01 2.01e+02 angle pdb=" CA VAL B 78 " pdb=" C VAL B 78 " pdb=" O VAL B 78 " ideal model delta sigma weight residual 119.95 105.01 14.94 1.34e+00 5.57e-01 1.24e+02 angle pdb=" O MET A 338 " pdb=" C MET A 338 " pdb=" N PRO A 339 " ideal model delta sigma weight residual 121.32 112.40 8.92 9.10e-01 1.21e+00 9.60e+01 angle pdb=" C MET B 80 " pdb=" N ASP B 81 " pdb=" CA ASP B 81 " ideal model delta sigma weight residual 120.68 136.43 -15.75 1.70e+00 3.46e-01 8.58e+01 angle pdb=" N GLY A 348 " pdb=" CA GLY A 348 " pdb=" C GLY A 348 " ideal model delta sigma weight residual 115.43 102.92 12.51 1.41e+00 5.03e-01 7.87e+01 ... (remaining 22259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.99: 10054 27.99 - 55.97: 613 55.97 - 83.96: 56 83.96 - 111.94: 3 111.94 - 139.93: 2 Dihedral angle restraints: 10728 sinusoidal: 5081 harmonic: 5647 Sorted by residual: dihedral pdb=" CA ALA A 349 " pdb=" C ALA A 349 " pdb=" N TYR A 350 " pdb=" CA TYR A 350 " ideal model delta harmonic sigma weight residual 180.00 -129.36 -50.64 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA LYS B 329 " pdb=" C LYS B 329 " pdb=" N CYS B 330 " pdb=" CA CYS B 330 " ideal model delta harmonic sigma weight residual 180.00 132.79 47.21 0 5.00e+00 4.00e-02 8.92e+01 dihedral pdb=" CB CYS B 330 " pdb=" SG CYS B 330 " pdb=" SG CYS B 352 " pdb=" CB CYS B 352 " ideal model delta sinusoidal sigma weight residual 93.00 9.92 83.08 1 1.00e+01 1.00e-02 8.44e+01 ... (remaining 10725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.002: 2539 1.002 - 2.004: 4 2.004 - 3.006: 0 3.006 - 4.008: 0 4.008 - 5.010: 1 Chirality restraints: 2544 Sorted by residual: chirality pdb=" CI4 PII A 812 " pdb=" CI3 PII A 812 " pdb=" CI5 PII A 812 " pdb=" OI4 PII A 812 " both_signs ideal model delta sigma weight residual False 2.51 -2.50 5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C2 PEE A 811 " pdb=" C1 PEE A 811 " pdb=" C3 PEE A 811 " pdb=" O2 PEE A 811 " both_signs ideal model delta sigma weight residual False -2.33 -0.50 -1.83 2.00e-01 2.50e+01 8.38e+01 chirality pdb=" C17 CLR A 802 " pdb=" C13 CLR A 802 " pdb=" C16 CLR A 802 " pdb=" C20 CLR A 802 " both_signs ideal model delta sigma weight residual False 2.55 0.83 1.72 2.00e-01 2.50e+01 7.39e+01 ... (remaining 2541 not shown) Planarity restraints: 2675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 346 " 0.037 2.00e-02 2.50e+03 7.62e-02 5.80e+01 pdb=" C VAL A 346 " -0.132 2.00e-02 2.50e+03 pdb=" O VAL A 346 " 0.050 2.00e-02 2.50e+03 pdb=" N LEU A 347 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 78 " -0.033 2.00e-02 2.50e+03 6.77e-02 4.58e+01 pdb=" C VAL B 78 " 0.117 2.00e-02 2.50e+03 pdb=" O VAL B 78 " -0.040 2.00e-02 2.50e+03 pdb=" N PRO B 79 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 80 " -0.032 2.00e-02 2.50e+03 6.60e-02 4.36e+01 pdb=" C MET B 80 " 0.114 2.00e-02 2.50e+03 pdb=" O MET B 80 " -0.041 2.00e-02 2.50e+03 pdb=" N ASP B 81 " -0.041 2.00e-02 2.50e+03 ... (remaining 2672 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 145 2.59 - 3.17: 14729 3.17 - 3.75: 23222 3.75 - 4.32: 32976 4.32 - 4.90: 52796 Nonbonded interactions: 123868 Sorted by model distance: nonbonded pdb=" O ILE A 340 " pdb=" CD LYS A 341 " model vdw 2.017 3.440 nonbonded pdb=" O VAL B 78 " pdb=" O PRO B 79 " model vdw 2.208 3.040 nonbonded pdb=" O VAL B 78 " pdb=" OD1 ASP B 81 " model vdw 2.289 3.040 nonbonded pdb=" O GLY A 342 " pdb=" N GLU A 351 " model vdw 2.305 3.120 nonbonded pdb=" O THR A 130 " pdb=" OD1 ASN A 134 " model vdw 2.324 3.040 ... (remaining 123863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 66 through 199 or (resid 200 and (name N or name CA or nam \ e C or name O or name CB )) or resid 201 through 235 or resid 238 through 404 or \ (resid 405 through 408 and (name N or name CA or name C or name O or name CB )) \ or resid 409 through 528 or (resid 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 670 or resid 712 through 730 or resid 801 \ through 810)) selection = (chain 'B' and (resid 66 through 234 or resid 258 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 406 or \ (resid 407 through 408 and (name N or name CA or name C or name O or name CB )) \ or resid 409 through 810)) } ncs_group { reference = (chain 'H' and ((resid 2 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or resid 3 through 122)) selection = chain 'I' } 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: 2.500 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: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.120 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4540 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 : 0.005 0.186 16336 Z= 0.309 Angle : 0.979 22.561 22292 Z= 0.547 Chirality : 0.130 5.010 2544 Planarity : 0.006 0.081 2675 Dihedral : 15.918 139.928 7046 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 1.31 % Allowed : 16.80 % Favored : 81.89 % Rotamer: Outliers : 1.72 % Allowed : 14.90 % Favored : 83.37 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.18), residues: 1911 helix: -1.92 (0.20), residues: 603 sheet: -1.55 (0.34), residues: 222 loop : -3.13 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 53 TYR 0.045 0.001 TYR B 350 PHE 0.017 0.001 PHE C 196 TRP 0.012 0.001 TRP D 352 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.31 (16322) covalent geometry : angle 0.97633 / 0.55 (22264) SS BOND : bond 0.00892 / 0.45 ( 14) SS BOND : angle 2.12899 / 1.38 ( 28) hydrogen bonds : bond 0.19706 / 13.46 ( 447) hydrogen bonds : angle 8.03402 / 5.76 ( 1251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 382 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: -0.0499 (ptm) cc_final: -0.0975 (mtp) REVERT: B 457 THR cc_start: 0.8371 (p) cc_final: 0.8162 (p) REVERT: B 558 LEU cc_start: 0.7178 (mt) cc_final: 0.6729 (mt) REVERT: A 471 ILE cc_start: 0.8382 (mm) cc_final: 0.8165 (mm) REVERT: A 486 TRP cc_start: 0.7774 (m100) cc_final: 0.7139 (t-100) REVERT: A 577 ARG cc_start: 0.6908 (tpp-160) cc_final: 0.6026 (tpp80) REVERT: A 597 CYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7566 (m) REVERT: C 85 MET cc_start: 0.4497 (mtt) cc_final: 0.4070 (mmm) REVERT: D 107 TRP cc_start: 0.6245 (m100) cc_final: 0.5059 (m100) REVERT: D 226 MET cc_start: -0.2321 (mtp) cc_final: -0.2592 (mtt) REVERT: I 86 MET cc_start: -0.1552 (mmp) cc_final: -0.2006 (mmm) REVERT: I 103 ASP cc_start: -0.2696 (OUTLIER) cc_final: -0.3632 (m-30) outliers start: 28 outliers final: 6 residues processed: 399 average time/residue: 0.1183 time to fit residues: 69.0944 Evaluate side-chains 212 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS B 98 ASN B 158 GLN B 193 GLN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 440 HIS B 652 HIS B 669 HIS A 151 GLN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN A 650 HIS ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN D 189 GLN D 243 ASN D 324 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.241958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.195144 restraints weight = 47676.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.200669 restraints weight = 24722.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.204265 restraints weight = 15011.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.206659 restraints weight = 10118.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.208000 restraints weight = 7450.625| |-----------------------------------------------------------------------------| r_work (final): 0.4781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16336 Z= 0.188 Angle : 0.891 13.866 22292 Z= 0.449 Chirality : 0.050 0.310 2544 Planarity : 0.006 0.068 2675 Dihedral : 10.350 110.478 3599 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.68 % Allowed : 16.64 % Favored : 82.68 % Rotamer: Outliers : 0.37 % Allowed : 5.36 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.18), residues: 1911 helix: -1.38 (0.19), residues: 632 sheet: -1.57 (0.34), residues: 235 loop : -3.23 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 528 TYR 0.019 0.002 TYR A 350 PHE 0.032 0.002 PHE A 538 TRP 0.031 0.002 TRP C 121 HIS 0.011 0.002 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (16322) covalent geometry : angle 0.88886 / 0.45 (22264) SS BOND : bond 0.00670 / 0.39 ( 14) SS BOND : angle 1.96440 / 1.33 ( 28) hydrogen bonds : bond 0.05404 / 3.58 ( 447) hydrogen bonds : angle 5.61218 / 4.03 ( 1251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 265 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: -0.0690 (ptm) cc_final: -0.1306 (mtp) REVERT: B 489 LEU cc_start: 0.8244 (mt) cc_final: 0.7924 (mt) REVERT: B 578 TRP cc_start: 0.7720 (m100) cc_final: 0.7412 (m100) REVERT: B 590 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7405 (mt) REVERT: A 162 TRP cc_start: 0.7109 (t-100) cc_final: 0.6851 (t-100) REVERT: A 418 LEU cc_start: 0.7993 (tt) cc_final: 0.7314 (pp) REVERT: A 452 LEU cc_start: 0.5665 (mp) cc_final: 0.4505 (mp) REVERT: A 643 MET cc_start: 0.8921 (ttt) cc_final: 0.8296 (ttt) REVERT: C 65 TRP cc_start: 0.6684 (t60) cc_final: 0.6480 (t60) REVERT: C 85 MET cc_start: 0.6308 (mtt) cc_final: 0.5337 (mmm) REVERT: D 97 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7543 (tptp) REVERT: D 151 MET cc_start: 0.5338 (mmp) cc_final: 0.4814 (mmp) REVERT: D 222 MET cc_start: 0.5871 (tpp) cc_final: 0.5341 (tpp) REVERT: H 35 MET cc_start: 0.0879 (tpp) cc_final: 0.0618 (tpp) outliers start: 6 outliers final: 0 residues processed: 269 average time/residue: 0.1066 time to fit residues: 43.3159 Evaluate side-chains 203 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 192 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 164 optimal weight: 20.0000 chunk 141 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 HIS B 639 GLN B 652 HIS ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 HIS A 650 HIS A 736 ASN A 737 ASN C 69 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.240749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.192427 restraints weight = 48111.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.197865 restraints weight = 25334.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.201191 restraints weight = 15590.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.203548 restraints weight = 10839.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.204943 restraints weight = 8193.753| |-----------------------------------------------------------------------------| r_work (final): 0.4742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5529 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16336 Z= 0.162 Angle : 0.811 11.881 22292 Z= 0.407 Chirality : 0.048 0.349 2544 Planarity : 0.006 0.087 2675 Dihedral : 9.834 101.732 3599 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.68 % Allowed : 16.69 % Favored : 82.63 % Rotamer: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.18), residues: 1911 helix: -0.95 (0.20), residues: 630 sheet: -1.92 (0.33), residues: 239 loop : -3.05 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 264 TYR 0.044 0.002 TYR C 90 PHE 0.056 0.002 PHE A 538 TRP 0.017 0.002 TRP C 116 HIS 0.007 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (16322) covalent geometry : angle 0.80831 / 0.41 (22264) SS BOND : bond 0.01125 / 0.77 ( 14) SS BOND : angle 2.10699 / 1.52 ( 28) hydrogen bonds : bond 0.04584 / 2.98 ( 447) hydrogen bonds : angle 5.29668 / 3.83 ( 1251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: -0.0658 (ptm) cc_final: -0.1188 (tpp) REVERT: B 420 ILE cc_start: 0.7330 (mp) cc_final: 0.6976 (mp) REVERT: B 467 PHE cc_start: 0.8105 (m-10) cc_final: 0.7866 (m-80) REVERT: B 578 TRP cc_start: 0.7802 (m100) cc_final: 0.7499 (m100) REVERT: B 645 MET cc_start: 0.7649 (ptm) cc_final: 0.7384 (ppp) REVERT: A 418 LEU cc_start: 0.7940 (tt) cc_final: 0.7240 (pp) REVERT: A 489 LEU cc_start: 0.9239 (mp) cc_final: 0.8996 (mp) REVERT: A 542 ILE cc_start: 0.9086 (tp) cc_final: 0.8883 (mm) REVERT: C 66 LEU cc_start: 0.8812 (mt) cc_final: 0.8550 (mt) REVERT: C 85 MET cc_start: 0.6604 (mtt) cc_final: 0.6180 (tpp) REVERT: C 116 TRP cc_start: 0.5173 (m100) cc_final: 0.4945 (m100) REVERT: D 97 LYS cc_start: 0.7855 (mmtp) cc_final: 0.7527 (mmtm) REVERT: D 107 TRP cc_start: 0.6862 (m100) cc_final: 0.4402 (t60) REVERT: D 109 MET cc_start: -0.4172 (tpp) cc_final: -0.4444 (tpp) REVERT: D 151 MET cc_start: 0.5558 (mmp) cc_final: 0.5016 (mmp) REVERT: D 222 MET cc_start: 0.5841 (tpp) cc_final: 0.5220 (tpp) REVERT: D 326 ASN cc_start: 0.8138 (m110) cc_final: 0.7894 (t0) REVERT: H 35 MET cc_start: 0.0706 (tpp) cc_final: 0.0458 (tpp) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.1088 time to fit residues: 41.4270 Evaluate side-chains 188 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 66 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 70 optimal weight: 30.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 309 ASN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.232837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.184778 restraints weight = 48709.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.184504 restraints weight = 31795.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.188323 restraints weight = 20522.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.188711 restraints weight = 13894.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.188740 restraints weight = 12522.905| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16336 Z= 0.202 Angle : 0.857 9.746 22292 Z= 0.435 Chirality : 0.050 0.309 2544 Planarity : 0.006 0.062 2675 Dihedral : 9.758 118.993 3599 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.68 % Allowed : 17.11 % Favored : 82.21 % Rotamer: Outliers : 0.18 % Allowed : 5.79 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.19), residues: 1911 helix: -0.74 (0.20), residues: 624 sheet: -1.42 (0.34), residues: 231 loop : -3.01 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 525 TYR 0.028 0.002 TYR B 722 PHE 0.032 0.002 PHE B 492 TRP 0.026 0.002 TRP B 486 HIS 0.008 0.002 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (16322) covalent geometry : angle 0.85544 / 0.43 (22264) SS BOND : bond 0.00590 / 0.36 ( 14) SS BOND : angle 1.84972 / 1.40 ( 28) hydrogen bonds : bond 0.04753 / 3.14 ( 447) hydrogen bonds : angle 5.37516 / 3.87 ( 1251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 221 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: -0.0874 (ptm) cc_final: -0.1598 (mmm) REVERT: B 423 PHE cc_start: 0.7874 (t80) cc_final: 0.7642 (t80) REVERT: B 467 PHE cc_start: 0.8065 (m-10) cc_final: 0.7829 (m-80) REVERT: B 486 TRP cc_start: 0.7768 (m-10) cc_final: 0.7504 (m-10) REVERT: B 645 MET cc_start: 0.7846 (ptm) cc_final: 0.7511 (ppp) REVERT: B 647 TYR cc_start: 0.8036 (m-80) cc_final: 0.7353 (m-80) REVERT: A 632 PHE cc_start: 0.8170 (m-10) cc_final: 0.7826 (m-80) REVERT: C 66 LEU cc_start: 0.9084 (mt) cc_final: 0.8871 (mt) REVERT: C 85 MET cc_start: 0.6873 (mtt) cc_final: 0.6577 (mtm) REVERT: C 115 PHE cc_start: 0.7143 (m-80) cc_final: 0.6940 (m-10) REVERT: C 116 TRP cc_start: 0.5629 (m100) cc_final: 0.4587 (m100) REVERT: D 222 MET cc_start: 0.6002 (tpp) cc_final: 0.5403 (tpp) REVERT: D 326 ASN cc_start: 0.8514 (m110) cc_final: 0.8278 (m-40) REVERT: H 35 MET cc_start: 0.0855 (tpp) cc_final: 0.0648 (tpp) outliers start: 3 outliers final: 1 residues processed: 223 average time/residue: 0.1068 time to fit residues: 37.4813 Evaluate side-chains 172 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 55 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 HIS B 158 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS B 652 HIS ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.231298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.181020 restraints weight = 48712.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.182002 restraints weight = 33883.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.186878 restraints weight = 20358.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.186433 restraints weight = 14598.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.186568 restraints weight = 12652.335| |-----------------------------------------------------------------------------| r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16336 Z= 0.182 Angle : 0.806 10.517 22292 Z= 0.407 Chirality : 0.048 0.245 2544 Planarity : 0.005 0.074 2675 Dihedral : 9.619 128.799 3599 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.68 % Allowed : 16.85 % Favored : 82.47 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.19), residues: 1911 helix: -0.55 (0.20), residues: 632 sheet: -1.47 (0.33), residues: 243 loop : -3.06 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 135 TYR 0.026 0.002 TYR B 722 PHE 0.033 0.002 PHE A 538 TRP 0.020 0.002 TRP D 107 HIS 0.006 0.001 HIS B 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (16322) covalent geometry : angle 0.80338 / 0.41 (22264) SS BOND : bond 0.00951 / 0.58 ( 14) SS BOND : angle 2.14577 / 1.56 ( 28) hydrogen bonds : bond 0.04313 / 2.88 ( 447) hydrogen bonds : angle 5.26840 / 3.80 ( 1251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: -0.0940 (ptm) cc_final: -0.1619 (mmm) REVERT: B 423 PHE cc_start: 0.7729 (t80) cc_final: 0.7342 (t80) REVERT: B 521 MET cc_start: 0.4771 (ppp) cc_final: 0.4373 (ppp) REVERT: B 652 HIS cc_start: 0.7179 (m90) cc_final: 0.6329 (m-70) REVERT: C 85 MET cc_start: 0.6948 (mtt) cc_final: 0.6131 (tpp) REVERT: C 112 THR cc_start: 0.4242 (t) cc_final: 0.3840 (t) REVERT: C 116 TRP cc_start: 0.5540 (m100) cc_final: 0.4606 (m100) REVERT: D 222 MET cc_start: 0.6288 (tpp) cc_final: 0.5725 (tpp) REVERT: D 326 ASN cc_start: 0.8468 (m110) cc_final: 0.8158 (m-40) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1176 time to fit residues: 39.1673 Evaluate side-chains 172 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 30 optimal weight: 9.9990 chunk 160 optimal weight: 0.4980 chunk 108 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 14 optimal weight: 0.0770 chunk 156 optimal weight: 20.0000 chunk 25 optimal weight: 0.0980 chunk 126 optimal weight: 20.0000 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 HIS A 650 HIS A 737 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5049 r_free = 0.5049 target = 0.233693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.184654 restraints weight = 48482.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.188277 restraints weight = 27109.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.189514 restraints weight = 18582.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.191582 restraints weight = 14462.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.192751 restraints weight = 9929.660| |-----------------------------------------------------------------------------| r_work (final): 0.4584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16336 Z= 0.139 Angle : 0.769 9.772 22292 Z= 0.385 Chirality : 0.047 0.331 2544 Planarity : 0.005 0.076 2675 Dihedral : 9.290 117.582 3599 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.58 % Allowed : 17.01 % Favored : 82.42 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.19), residues: 1911 helix: -0.41 (0.21), residues: 630 sheet: -1.52 (0.33), residues: 234 loop : -3.05 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 577 TYR 0.018 0.001 TYR I 104 PHE 0.038 0.002 PHE A 538 TRP 0.031 0.001 TRP D 107 HIS 0.011 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (16322) covalent geometry : angle 0.76360 / 0.38 (22264) SS BOND : bond 0.00626 / 0.43 ( 14) SS BOND : angle 2.61714 / 1.93 ( 28) hydrogen bonds : bond 0.03894 / 2.59 ( 447) hydrogen bonds : angle 4.97371 / 3.57 ( 1251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: -0.0896 (ptm) cc_final: -0.1624 (mmm) REVERT: B 423 PHE cc_start: 0.7844 (t80) cc_final: 0.7224 (t80) REVERT: A 339 PRO cc_start: 0.6649 (Cg_endo) cc_final: 0.6298 (Cg_exo) REVERT: A 643 MET cc_start: 0.8279 (tmm) cc_final: 0.8039 (tmm) REVERT: C 27 MET cc_start: 0.3759 (ttt) cc_final: 0.3380 (tmm) REVERT: C 85 MET cc_start: 0.7143 (mtt) cc_final: 0.6377 (tpp) REVERT: C 116 TRP cc_start: 0.5266 (m100) cc_final: 0.4537 (m100) REVERT: D 180 TRP cc_start: 0.3029 (m100) cc_final: 0.2752 (m100) REVERT: D 222 MET cc_start: 0.6260 (tpp) cc_final: 0.5580 (tpp) REVERT: D 326 ASN cc_start: 0.8384 (m110) cc_final: 0.7844 (t0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1067 time to fit residues: 35.5616 Evaluate side-chains 169 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 187 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 121 optimal weight: 0.1980 chunk 35 optimal weight: 7.9990 chunk 84 optimal weight: 0.3980 chunk 177 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 HIS B 328 HIS ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN I 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5342 r_free = 0.5342 target = 0.302633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5244 r_free = 0.5244 target = 0.279510 restraints weight = 65264.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5266 r_free = 0.5266 target = 0.278769 restraints weight = 85948.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5264 r_free = 0.5264 target = 0.278442 restraints weight = 65091.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5262 r_free = 0.5262 target = 0.278530 restraints weight = 57340.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5265 r_free = 0.5265 target = 0.278600 restraints weight = 48458.742| |-----------------------------------------------------------------------------| r_work (final): 0.4769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5218 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16336 Z= 0.146 Angle : 0.770 9.885 22292 Z= 0.388 Chirality : 0.046 0.218 2544 Planarity : 0.005 0.076 2675 Dihedral : 9.087 112.588 3599 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.58 % Allowed : 17.43 % Favored : 82.00 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.19), residues: 1911 helix: -0.31 (0.21), residues: 640 sheet: -1.41 (0.33), residues: 243 loop : -3.05 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 631 TYR 0.019 0.001 TYR C 90 PHE 0.037 0.002 PHE A 538 TRP 0.032 0.001 TRP D 107 HIS 0.009 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (16322) covalent geometry : angle 0.76635 / 0.39 (22264) SS BOND : bond 0.00527 / 0.30 ( 14) SS BOND : angle 2.28421 / 1.68 ( 28) hydrogen bonds : bond 0.03755 / 2.52 ( 447) hydrogen bonds : angle 4.93361 / 3.55 ( 1251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.0279 (ptm) cc_final: -0.0996 (mmm) REVERT: B 423 PHE cc_start: 0.8052 (t80) cc_final: 0.7377 (t80) REVERT: B 578 TRP cc_start: 0.8180 (m100) cc_final: 0.7806 (m100) REVERT: B 581 MET cc_start: 0.8239 (mmp) cc_final: 0.7884 (mmt) REVERT: B 652 HIS cc_start: 0.7480 (m-70) cc_final: 0.7179 (m-70) REVERT: A 542 ILE cc_start: 0.8956 (tp) cc_final: 0.8697 (tp) REVERT: A 643 MET cc_start: 0.8784 (tmm) cc_final: 0.8401 (tmm) REVERT: C 85 MET cc_start: 0.7210 (mtt) cc_final: 0.6487 (tpp) REVERT: C 116 TRP cc_start: 0.4896 (m100) cc_final: 0.4149 (m100) REVERT: D 222 MET cc_start: 0.5707 (tpp) cc_final: 0.5172 (tpp) REVERT: D 326 ASN cc_start: 0.8155 (m110) cc_final: 0.7555 (t0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1058 time to fit residues: 32.0114 Evaluate side-chains 163 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 151 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 0.0770 chunk 153 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 10 optimal weight: 0.4980 chunk 88 optimal weight: 0.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN A 193 GLN ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN D 189 GLN I 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.301878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5250 r_free = 0.5250 target = 0.278195 restraints weight = 65841.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5266 r_free = 0.5266 target = 0.278229 restraints weight = 92392.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.5261 r_free = 0.5261 target = 0.278012 restraints weight = 69649.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5261 r_free = 0.5261 target = 0.278152 restraints weight = 58336.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5263 r_free = 0.5263 target = 0.278223 restraints weight = 50427.109| |-----------------------------------------------------------------------------| r_work (final): 0.4737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5232 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16336 Z= 0.142 Angle : 0.760 10.232 22292 Z= 0.381 Chirality : 0.046 0.202 2544 Planarity : 0.005 0.094 2675 Dihedral : 8.928 111.566 3599 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.52 % Allowed : 17.22 % Favored : 82.26 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.19), residues: 1911 helix: -0.19 (0.21), residues: 636 sheet: -1.26 (0.34), residues: 239 loop : -3.06 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.033 0.001 TYR C 90 PHE 0.037 0.002 PHE A 538 TRP 0.016 0.001 TRP D 107 HIS 0.009 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (16322) covalent geometry : angle 0.75625 / 0.38 (22264) SS BOND : bond 0.00592 / 0.35 ( 14) SS BOND : angle 2.14987 / 1.57 ( 28) hydrogen bonds : bond 0.03679 / 2.48 ( 447) hydrogen bonds : angle 4.87650 / 3.50 ( 1251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 LEU cc_start: 0.7244 (tp) cc_final: 0.6954 (tp) REVERT: B 139 MET cc_start: 0.0158 (ptm) cc_final: -0.1108 (mmm) REVERT: B 423 PHE cc_start: 0.8018 (t80) cc_final: 0.7359 (t80) REVERT: B 527 MET cc_start: 0.9120 (tpp) cc_final: 0.8886 (tpp) REVERT: B 530 LEU cc_start: 0.9533 (tp) cc_final: 0.9314 (tp) REVERT: B 578 TRP cc_start: 0.8262 (m100) cc_final: 0.7869 (m100) REVERT: B 581 MET cc_start: 0.8304 (mmp) cc_final: 0.7973 (mmt) REVERT: B 588 LEU cc_start: 0.9458 (mt) cc_final: 0.9245 (mt) REVERT: B 652 HIS cc_start: 0.7483 (m-70) cc_final: 0.7040 (m-70) REVERT: A 435 MET cc_start: 0.8667 (ttm) cc_final: 0.8467 (ttm) REVERT: A 542 ILE cc_start: 0.9113 (tp) cc_final: 0.8870 (tp) REVERT: A 643 MET cc_start: 0.8841 (tmm) cc_final: 0.8454 (tmm) REVERT: C 85 MET cc_start: 0.7159 (mtt) cc_final: 0.6529 (tpt) REVERT: C 91 PHE cc_start: 0.2786 (p90) cc_final: 0.2556 (p90) REVERT: C 116 TRP cc_start: 0.4791 (m100) cc_final: 0.4107 (m100) REVERT: D 222 MET cc_start: 0.5692 (tpp) cc_final: 0.5159 (tpp) REVERT: D 326 ASN cc_start: 0.8211 (m110) cc_final: 0.7695 (m-40) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1051 time to fit residues: 32.7767 Evaluate side-chains 170 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 59 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 136 optimal weight: 0.3980 chunk 124 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN B 652 HIS ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS A 123 HIS A 131 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.289763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5134 r_free = 0.5134 target = 0.264808 restraints weight = 65486.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.264734 restraints weight = 99406.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5148 r_free = 0.5148 target = 0.264979 restraints weight = 77173.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.5143 r_free = 0.5143 target = 0.264286 restraints weight = 69770.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.264412 restraints weight = 67424.767| |-----------------------------------------------------------------------------| r_work (final): 0.4628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5480 moved from start: 0.7926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16336 Z= 0.215 Angle : 0.901 10.303 22292 Z= 0.456 Chirality : 0.051 0.237 2544 Planarity : 0.006 0.090 2675 Dihedral : 9.725 107.589 3599 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.63 % Allowed : 18.11 % Favored : 81.27 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.18), residues: 1911 helix: -0.74 (0.20), residues: 619 sheet: -1.13 (0.36), residues: 214 loop : -3.12 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 44 TYR 0.018 0.002 TYR B 157 PHE 0.025 0.003 PHE D 254 TRP 0.026 0.003 TRP D 180 HIS 0.009 0.002 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (16322) covalent geometry : angle 0.89907 / 0.45 (22264) SS BOND : bond 0.01220 / 0.64 ( 14) SS BOND : angle 2.06516 / 1.49 ( 28) hydrogen bonds : bond 0.04976 / 3.29 ( 447) hydrogen bonds : angle 5.51987 / 3.95 ( 1251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.0872 (ptm) cc_final: -0.0737 (mmt) REVERT: B 423 PHE cc_start: 0.8057 (t80) cc_final: 0.7441 (t80) REVERT: B 521 MET cc_start: 0.4763 (ppp) cc_final: 0.4544 (ppp) REVERT: B 534 LEU cc_start: 0.9402 (mt) cc_final: 0.9164 (tt) REVERT: B 578 TRP cc_start: 0.8366 (m100) cc_final: 0.7984 (m100) REVERT: B 581 MET cc_start: 0.8428 (mmp) cc_final: 0.8118 (mmt) REVERT: B 652 HIS cc_start: 0.7348 (m90) cc_final: 0.6824 (m90) REVERT: A 542 ILE cc_start: 0.9335 (tp) cc_final: 0.9134 (tp) REVERT: A 733 MET cc_start: 0.4526 (tpt) cc_final: 0.4303 (tpp) REVERT: C 57 PHE cc_start: 0.4483 (p90) cc_final: 0.4243 (p90) REVERT: C 85 MET cc_start: 0.7883 (mtt) cc_final: 0.7261 (tpt) REVERT: C 116 TRP cc_start: 0.5125 (m100) cc_final: 0.4230 (m100) REVERT: D 222 MET cc_start: 0.5459 (tpp) cc_final: 0.5023 (tpp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1175 time to fit residues: 36.7680 Evaluate side-chains 149 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 56 optimal weight: 0.0060 chunk 178 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 HIS ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN A 131 HIS A 193 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.295531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5184 r_free = 0.5184 target = 0.272291 restraints weight = 65349.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5213 r_free = 0.5213 target = 0.271419 restraints weight = 84497.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5200 r_free = 0.5200 target = 0.270772 restraints weight = 73333.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5201 r_free = 0.5201 target = 0.271104 restraints weight = 67228.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.271080 restraints weight = 52364.075| |-----------------------------------------------------------------------------| r_work (final): 0.4662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5389 moved from start: 0.8058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16336 Z= 0.141 Angle : 0.789 11.375 22292 Z= 0.394 Chirality : 0.047 0.273 2544 Planarity : 0.005 0.093 2675 Dihedral : 9.183 111.658 3599 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.52 % Allowed : 16.95 % Favored : 82.52 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.18), residues: 1911 helix: -0.55 (0.20), residues: 629 sheet: -0.85 (0.37), residues: 196 loop : -3.11 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 577 TYR 0.027 0.001 TYR A 85 PHE 0.040 0.002 PHE A 538 TRP 0.021 0.001 TRP B 486 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (16322) covalent geometry : angle 0.78604 / 0.39 (22264) SS BOND : bond 0.00538 / 0.30 ( 14) SS BOND : angle 2.12898 / 1.64 ( 28) hydrogen bonds : bond 0.03839 / 2.58 ( 447) hydrogen bonds : angle 5.18443 / 3.72 ( 1251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.0904 (ptm) cc_final: -0.0565 (mmm) REVERT: B 423 PHE cc_start: 0.8043 (t80) cc_final: 0.7264 (t80) REVERT: B 534 LEU cc_start: 0.9399 (mt) cc_final: 0.9131 (tt) REVERT: B 578 TRP cc_start: 0.8274 (m100) cc_final: 0.7882 (m100) REVERT: B 581 MET cc_start: 0.8562 (mmp) cc_final: 0.8227 (mmt) REVERT: B 588 LEU cc_start: 0.9466 (mt) cc_final: 0.9257 (mt) REVERT: B 595 TYR cc_start: 0.6974 (t80) cc_final: 0.6677 (t80) REVERT: B 643 MET cc_start: 0.8775 (ppp) cc_final: 0.8541 (ppp) REVERT: B 652 HIS cc_start: 0.7551 (m90) cc_final: 0.6941 (m90) REVERT: A 462 SER cc_start: 0.8950 (m) cc_final: 0.8722 (p) REVERT: A 577 ARG cc_start: 0.8051 (tpp-160) cc_final: 0.7578 (tpp-160) REVERT: A 580 TYR cc_start: 0.7637 (m-10) cc_final: 0.7407 (m-10) REVERT: A 666 LYS cc_start: 0.8248 (pptt) cc_final: 0.7834 (mtpt) REVERT: C 85 MET cc_start: 0.7763 (mtt) cc_final: 0.7222 (tpt) REVERT: C 88 HIS cc_start: 0.8694 (m90) cc_final: 0.8456 (m90) REVERT: C 116 TRP cc_start: 0.5335 (m100) cc_final: 0.4362 (m100) REVERT: D 222 MET cc_start: 0.5493 (tpp) cc_final: 0.5034 (tpp) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1092 time to fit residues: 32.9722 Evaluate side-chains 163 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 30 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 31 optimal weight: 0.0070 chunk 184 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 14 optimal weight: 0.0000 chunk 106 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 overall best weight: 0.7806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.222300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.177017 restraints weight = 47519.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.172423 restraints weight = 24466.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.173789 restraints weight = 20987.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.174157 restraints weight = 15651.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.174386 restraints weight = 14569.194| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.8192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16336 Z= 0.136 Angle : 0.776 10.704 22292 Z= 0.387 Chirality : 0.046 0.215 2544 Planarity : 0.005 0.085 2675 Dihedral : 8.962 109.513 3599 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.47 % Allowed : 17.32 % Favored : 82.21 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.19), residues: 1911 helix: -0.37 (0.20), residues: 630 sheet: -0.81 (0.37), residues: 194 loop : -3.08 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 488 TYR 0.023 0.001 TYR A 85 PHE 0.038 0.002 PHE A 538 TRP 0.019 0.001 TRP B 486 HIS 0.009 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (16322) covalent geometry : angle 0.77284 / 0.39 (22264) SS BOND : bond 0.00533 / 0.33 ( 14) SS BOND : angle 2.00712 / 1.49 ( 28) hydrogen bonds : bond 0.03704 / 2.46 ( 447) hydrogen bonds : angle 5.04488 / 3.60 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2784.66 seconds wall clock time: 48 minutes 45.94 seconds (2925.94 seconds total)