Starting phenix.real_space_refine on Thu Jul 2 17:01:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7she_25125/07_2026/7she_25125.cif Found real_map, /net/cci-nas-00/data/ceres_data/7she_25125/07_2026/7she_25125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7she_25125/07_2026/7she_25125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7she_25125/07_2026/7she_25125.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7she_25125/07_2026/7she_25125.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7she_25125/07_2026/7she_25125.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7she_25125/07_2026/7she_25125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7she_25125/07_2026/7she_25125.map" } resolution = 3.4 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= 0.021 sd= 0.072 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 60 5.16 5 C 6036 2.51 5 N 1394 2.21 5 O 1498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8990 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4131 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 23, 'TRANS': 517} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 3, 'HIS:plan': 4, 'ASN:plan1': 4, 'GLU:plan': 5, 'PHE:plan': 2, 'TYR:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4136 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 23, 'TRANS': 516} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 3, 'GLU:plan': 5, 'PHE:plan': 2, 'TYR:plan': 3, 'ASP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 111 Chain: "A" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 415 Unusual residues: {'CLR': 11, 'EIJ': 1, 'PEE': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 308 Unusual residues: {'CLR': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 2.01, per 1000 atoms: 0.22 Number of scatterers: 8990 At special positions: 0 Unit cell: (60.237, 101.268, 173.727, 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 60 16.00 P 2 15.00 O 1498 8.00 N 1394 7.00 C 6036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 272 " distance=2.02 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=2.16 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 402 " distance=2.04 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS A 481 " - pdb=" SG CYS A 573 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 352 " distance=2.04 Simple disulfide: pdb=" SG CYS B 337 " - pdb=" SG CYS B 392 " distance=2.03 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 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 301.4 milliseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 46.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 66 through 76 removed outlier: 4.054A pdb=" N ALA A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.184A pdb=" N SER A 91 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS A 92 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 93 " --> pdb=" O ASP A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 93' Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.726A pdb=" N LEU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP A 127 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 removed outlier: 3.505A pdb=" N TRP A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.804A pdb=" N CYS A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 441 removed outlier: 3.582A pdb=" N ALA A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A 428 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 451 through 465 removed outlier: 3.768A pdb=" N THR A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.741A pdb=" N PHE A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 496 removed outlier: 4.762A pdb=" N ARG A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.696A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 549 removed outlier: 4.473A pdb=" N ILE A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 583 through 600 removed outlier: 3.648A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 634 removed outlier: 3.627A pdb=" N TYR A 612 " --> pdb=" O HIS A 608 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 616 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.996A pdb=" N LEU A 646 " --> pdb=" O TRP A 642 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 651 " --> pdb=" O TYR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 662 Processing helix chain 'A' and resid 663 through 668 removed outlier: 4.293A pdb=" N PHE A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 668' Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.769A pdb=" N ALA B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 120 through 139 removed outlier: 4.394A pdb=" N PHE B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.621A pdb=" N ASP B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 160 " --> pdb=" O TRP B 156 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 4.111A pdb=" N ILE B 353 " --> pdb=" O TYR B 350 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS B 354 " --> pdb=" O GLU B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 354' Processing helix chain 'B' and resid 413 through 418 removed outlier: 3.583A pdb=" N ARG B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 Processing helix chain 'B' and resid 425 through 441 removed outlier: 3.597A pdb=" N ASP B 431 " --> pdb=" O CYS B 427 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 451 removed outlier: 4.091A pdb=" N SER B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 removed outlier: 3.684A pdb=" N GLU B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 469 through 475 removed outlier: 4.346A pdb=" N PHE B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU B 475 " --> pdb=" O ILE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 514 removed outlier: 4.432A pdb=" N LEU B 484 " --> pdb=" O ARG B 480 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 485 " --> pdb=" O CYS B 481 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 490 " --> pdb=" O TRP B 486 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 495 " --> pdb=" O GLY B 491 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR B 500 " --> pdb=" O TYR B 496 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 501 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 549 removed outlier: 3.603A pdb=" N ALA B 531 " --> pdb=" O MET B 527 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 532 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 533 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 554 removed outlier: 3.620A pdb=" N GLU B 553 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 600 removed outlier: 3.515A pdb=" N LEU B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 591 " --> pdb=" O PHE B 587 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 597 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 598 " --> pdb=" O VAL B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 634 removed outlier: 3.634A pdb=" N ALA B 614 " --> pdb=" O PRO B 610 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 616 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 617 " --> pdb=" O MET B 613 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 622 " --> pdb=" O HIS B 618 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE B 627 " --> pdb=" O ILE B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 651 removed outlier: 3.748A pdb=" N THR B 651 " --> pdb=" O TYR B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 668 removed outlier: 4.060A pdb=" N PHE B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 663 through 668' Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 176 removed outlier: 4.598A pdb=" N ASP A 307 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA A 174 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS A 305 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE A 176 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL A 303 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 192 removed outlier: 4.510A pdb=" N VAL A 190 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 204 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 559 through 563 removed outlier: 4.301A pdb=" N GLY A 562 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.518A pdb=" N LEU B 202 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY B 302 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 560 through 561 264 hydrogen bonds defined for protein. 759 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: 0.98 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.09: 9 1.09 - 1.27: 1293 1.27 - 1.46: 3198 1.46 - 1.64: 4669 1.64 - 1.83: 92 Bond restraints: 9261 Sorted by residual: bond pdb=" C TRP A 642 " pdb=" O TRP A 642 " ideal model delta sigma weight residual 1.236 0.903 0.333 1.32e-02 5.74e+03 6.36e+02 bond pdb=" C PHE A 570 " pdb=" O PHE A 570 " ideal model delta sigma weight residual 1.234 0.952 0.282 1.18e-02 7.18e+03 5.71e+02 bond pdb=" C PRO A 476 " pdb=" O PRO A 476 " ideal model delta sigma weight residual 1.235 0.928 0.307 1.30e-02 5.92e+03 5.59e+02 bond pdb=" N PRO A 374 " pdb=" CA PRO A 374 " ideal model delta sigma weight residual 1.470 1.686 -0.216 1.01e-02 9.80e+03 4.56e+02 bond pdb=" N PRO B 374 " pdb=" CA PRO B 374 " ideal model delta sigma weight residual 1.469 1.691 -0.222 1.28e-02 6.10e+03 3.01e+02 ... (remaining 9256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.47: 12628 9.47 - 18.94: 62 18.94 - 28.41: 18 28.41 - 37.88: 2 37.88 - 47.35: 2 Bond angle restraints: 12712 Sorted by residual: angle pdb=" N TYR B 390 " pdb=" CA TYR B 390 " pdb=" C TYR B 390 " ideal model delta sigma weight residual 113.50 160.85 -47.35 1.23e+00 6.61e-01 1.48e+03 angle pdb=" N GLN A 516 " pdb=" CA GLN A 516 " pdb=" C GLN A 516 " ideal model delta sigma weight residual 113.23 152.37 -39.14 1.22e+00 6.72e-01 1.03e+03 angle pdb=" N ALA A 403 " pdb=" CA ALA A 403 " pdb=" C ALA A 403 " ideal model delta sigma weight residual 110.97 139.54 -28.57 1.09e+00 8.42e-01 6.87e+02 angle pdb=" N VAL B 391 " pdb=" CA VAL B 391 " pdb=" CB VAL B 391 " ideal model delta sigma weight residual 110.65 87.74 22.91 1.13e+00 7.83e-01 4.11e+02 angle pdb=" N ALA B 389 " pdb=" CA ALA B 389 " pdb=" C ALA B 389 " ideal model delta sigma weight residual 109.54 136.84 -27.30 1.37e+00 5.33e-01 3.97e+02 ... (remaining 12707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.43: 4930 26.43 - 52.87: 298 52.87 - 79.30: 49 79.30 - 105.73: 16 105.73 - 132.16: 14 Dihedral angle restraints: 5307 sinusoidal: 2160 harmonic: 3147 Sorted by residual: dihedral pdb=" C CYS A 402 " pdb=" N CYS A 402 " pdb=" CA CYS A 402 " pdb=" CB CYS A 402 " ideal model delta harmonic sigma weight residual -122.60 -164.59 41.99 0 2.50e+00 1.60e-01 2.82e+02 dihedral pdb=" N CYS A 402 " pdb=" C CYS A 402 " pdb=" CA CYS A 402 " pdb=" CB CYS A 402 " ideal model delta harmonic sigma weight residual 122.80 164.18 -41.38 0 2.50e+00 1.60e-01 2.74e+02 dihedral pdb=" C CYS B 99 " pdb=" N CYS B 99 " pdb=" CA CYS B 99 " pdb=" CB CYS B 99 " ideal model delta harmonic sigma weight residual -122.60 -88.09 -34.51 0 2.50e+00 1.60e-01 1.91e+02 ... (remaining 5304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.062: 1508 1.062 - 2.124: 3 2.124 - 3.186: 0 3.186 - 4.249: 0 4.249 - 5.311: 3 Chirality restraints: 1514 Sorted by residual: chirality pdb=" C8 CLR A 803 " pdb=" C14 CLR A 803 " pdb=" C7 CLR A 803 " pdb=" C9 CLR A 803 " both_signs ideal model delta sigma weight residual False 2.69 -2.62 5.31 2.00e-01 2.50e+01 7.05e+02 chirality pdb=" C8 CLR B 802 " pdb=" C14 CLR B 802 " pdb=" C7 CLR B 802 " pdb=" C9 CLR B 802 " both_signs ideal model delta sigma weight residual False 2.69 -2.62 5.31 2.00e-01 2.50e+01 7.05e+02 chirality pdb=" C17 CLR B 808 " pdb=" C13 CLR B 808 " pdb=" C16 CLR B 808 " pdb=" C20 CLR B 808 " both_signs ideal model delta sigma weight residual False 2.55 -2.57 5.12 2.00e-01 2.50e+01 6.55e+02 ... (remaining 1511 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 EIJ A 802 " 0.181 2.00e-02 2.50e+03 1.79e-01 3.21e+02 pdb=" C09 EIJ A 802 " -0.187 2.00e-02 2.50e+03 pdb=" C10 EIJ A 802 " -0.171 2.00e-02 2.50e+03 pdb=" C11 EIJ A 802 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 EIJ A 802 " 0.161 2.00e-02 2.50e+03 1.61e-01 2.58e+02 pdb=" C06 EIJ A 802 " -0.161 2.00e-02 2.50e+03 pdb=" C07 EIJ A 802 " -0.160 2.00e-02 2.50e+03 pdb=" C08 EIJ A 802 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 119 " 0.181 5.00e-02 4.00e+02 2.48e-01 9.81e+01 pdb=" N PRO A 120 " -0.424 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.164 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.079 5.00e-02 4.00e+02 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 8 2.18 - 2.86: 3063 2.86 - 3.54: 11610 3.54 - 4.22: 18676 4.22 - 4.90: 32151 Nonbonded interactions: 65508 Sorted by model distance: nonbonded pdb=" O GLN A 516 " pdb=" CG GLN A 516 " model vdw 1.502 3.440 nonbonded pdb=" SG CYS A 395 " pdb=" O CYS A 402 " model vdw 1.783 3.400 nonbonded pdb=" O PRO A 407 " pdb=" CD1 LEU A 568 " model vdw 1.866 3.460 nonbonded pdb=" N PHE A 474 " pdb=" O PHE A 474 " model vdw 1.930 2.496 nonbonded pdb=" CE1 TYR B 103 " pdb=" CB ALA B 106 " model vdw 2.091 3.760 ... (remaining 65503 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 205 or resid 261 through 352 or (resid 353 and \ (name N or name CA or name C or name O or name CB )) or resid 354 through 378 or \ (resid 379 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 0 through 670 or resid 803 through 811)) selection = (chain 'B' and (resid 66 through 292 or resid 298 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 331 or \ (resid 332 through 336 and (name N or name CA or name C or name O or name CB )) \ or resid 337 through 359 or (resid 360 and (name N or name CA or name C or name \ O or name CB )) or resid 361 through 362 or (resid 363 through 364 and (name N \ or name CA or name C or name O or name CB )) or resid 365 through 670 or resid 8 \ 03 through 811)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.890 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 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 : 0.016 0.693 9277 Z= 1.250 Angle : 1.786 47.349 12738 Z= 1.115 Chirality : 0.256 5.311 1514 Planarity : 0.013 0.248 1448 Dihedral : 18.512 132.163 3230 Min Nonbonded Distance : 1.502 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 1.88 % Allowed : 14.08 % Favored : 84.04 % Rotamer: Outliers : 1.41 % Allowed : 0.71 % Favored : 97.88 % Cbeta Deviations : 2.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.23), residues: 1065 helix: -2.12 (0.23), residues: 462 sheet: -1.40 (0.58), residues: 78 loop : -3.87 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 525 TYR 0.064 0.003 TYR B 269 PHE 0.077 0.002 PHE A 570 TRP 0.033 0.002 TRP A 642 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01308 / 0.89 ( 9261) covalent geometry : angle 1.78459 / 1.12 (12712) SS BOND : bond 0.03537 / 1.78 ( 13) SS BOND : angle 2.21101 / 1.41 ( 26) hydrogen bonds : bond 0.27779 / 19.63 ( 264) hydrogen bonds : angle 8.65513 / 6.11 ( 759) Misc. bond : bond 0.48923 / 23.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 VAL cc_start: 0.6445 (m) cc_final: 0.6226 (p) REVERT: A 602 THR cc_start: 0.8596 (p) cc_final: 0.8227 (m) REVERT: B 309 ASN cc_start: 0.7855 (t0) cc_final: 0.7421 (t0) outliers start: 12 outliers final: 5 residues processed: 157 average time/residue: 0.1044 time to fit residues: 21.5858 Evaluate side-chains 103 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 476 PRO Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 521 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0060 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN B 204 GLN B 333 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.152067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.118418 restraints weight = 15665.967| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.14 r_work: 0.3215 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9277 Z= 0.143 Angle : 0.789 10.267 12738 Z= 0.381 Chirality : 0.043 0.289 1514 Planarity : 0.007 0.129 1448 Dihedral : 15.643 124.687 1473 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 1.22 % Allowed : 14.37 % Favored : 84.41 % Rotamer: Outliers : 0.59 % Allowed : 8.00 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.29 % 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: -3.89 (0.24), residues: 1065 helix: -1.56 (0.23), residues: 479 sheet: -1.45 (0.54), residues: 88 loop : -3.95 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 173 TYR 0.012 0.001 TYR A 269 PHE 0.015 0.001 PHE A 423 TRP 0.012 0.001 TRP B 323 HIS 0.007 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 9261) covalent geometry : angle 0.78362 / 0.38 (12712) SS BOND : bond 0.00439 / 0.30 ( 13) SS BOND : angle 2.14737 / 1.24 ( 26) hydrogen bonds : bond 0.04732 / 3.26 ( 264) hydrogen bonds : angle 4.81675 / 3.35 ( 759) Misc. bond : bond 0.00052 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 THR cc_start: 0.9093 (p) cc_final: 0.8739 (m) REVERT: B 171 ILE cc_start: 0.7958 (tt) cc_final: 0.7505 (tt) REVERT: B 429 LEU cc_start: 0.8594 (tt) cc_final: 0.8266 (tp) outliers start: 5 outliers final: 2 residues processed: 100 average time/residue: 0.0833 time to fit residues: 11.6175 Evaluate side-chains 87 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 0.0570 chunk 56 optimal weight: 8.9990 chunk 15 optimal weight: 0.4980 chunk 55 optimal weight: 0.3980 chunk 85 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.151859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119173 restraints weight = 15404.476| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.56 r_work: 0.3242 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9277 Z= 0.123 Angle : 0.676 9.921 12738 Z= 0.333 Chirality : 0.040 0.211 1514 Planarity : 0.006 0.114 1448 Dihedral : 13.360 113.475 1462 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.33 % Favored : 85.45 % Rotamer: Outliers : 1.18 % Allowed : 9.41 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.10 % 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: -3.42 (0.25), residues: 1065 helix: -1.04 (0.24), residues: 490 sheet: -1.29 (0.57), residues: 88 loop : -3.90 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 442 TYR 0.008 0.001 TYR A 269 PHE 0.015 0.001 PHE A 423 TRP 0.011 0.001 TRP B 265 HIS 0.008 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9261) covalent geometry : angle 0.67219 / 0.33 (12712) SS BOND : bond 0.00247 / 0.17 ( 13) SS BOND : angle 1.63890 / 0.97 ( 26) hydrogen bonds : bond 0.03931 / 2.71 ( 264) hydrogen bonds : angle 4.29009 / 2.98 ( 759) Misc. bond : bond 0.00054 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TRP cc_start: 0.7366 (t60) cc_final: 0.6260 (t-100) REVERT: A 165 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6639 (mt) REVERT: A 166 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6391 (mp0) REVERT: A 315 ILE cc_start: 0.6390 (mp) cc_final: 0.6160 (tt) REVERT: B 122 LEU cc_start: 0.8184 (mm) cc_final: 0.7970 (mt) REVERT: B 304 MET cc_start: 0.7317 (tpp) cc_final: 0.6966 (tpp) REVERT: B 305 LYS cc_start: 0.7800 (ttmt) cc_final: 0.7515 (ptmt) REVERT: B 429 LEU cc_start: 0.8446 (tt) cc_final: 0.8130 (tp) outliers start: 10 outliers final: 5 residues processed: 99 average time/residue: 0.0957 time to fit residues: 13.3779 Evaluate side-chains 87 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.145320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.111193 restraints weight = 15250.393| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.25 r_work: 0.3059 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9277 Z= 0.200 Angle : 0.805 8.671 12738 Z= 0.389 Chirality : 0.044 0.201 1514 Planarity : 0.007 0.118 1448 Dihedral : 13.383 111.904 1462 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 1.03 % Allowed : 14.55 % Favored : 84.41 % Rotamer: Outliers : 2.00 % Allowed : 11.41 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.10 % 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: -3.40 (0.25), residues: 1065 helix: -0.98 (0.23), residues: 505 sheet: -1.26 (0.57), residues: 80 loop : -3.98 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 102 TYR 0.014 0.002 TYR B 473 PHE 0.025 0.002 PHE A 467 TRP 0.014 0.002 TRP B 265 HIS 0.007 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.20 ( 9261) covalent geometry : angle 0.80235 / 0.39 (12712) SS BOND : bond 0.00303 / 0.20 ( 13) SS BOND : angle 1.64035 / 1.00 ( 26) hydrogen bonds : bond 0.05699 / 3.99 ( 264) hydrogen bonds : angle 4.34126 / 3.04 ( 759) Misc. bond : bond 0.00085 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.7156 (mm) cc_final: 0.6927 (mp) REVERT: A 304 MET cc_start: 0.5546 (mmp) cc_final: 0.4882 (mmt) REVERT: B 304 MET cc_start: 0.8190 (tpp) cc_final: 0.7970 (tpp) REVERT: B 508 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8137 (mmtt) REVERT: B 528 ARG cc_start: 0.8406 (mtm180) cc_final: 0.8043 (mtm110) outliers start: 17 outliers final: 11 residues processed: 107 average time/residue: 0.0941 time to fit residues: 13.9484 Evaluate side-chains 105 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 538 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.145372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.112267 restraints weight = 15092.031| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.44 r_work: 0.3119 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9277 Z= 0.163 Angle : 0.722 8.774 12738 Z= 0.356 Chirality : 0.042 0.191 1514 Planarity : 0.006 0.103 1448 Dihedral : 12.938 113.634 1462 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.94 % Allowed : 13.90 % Favored : 85.16 % Rotamer: Outliers : 1.88 % Allowed : 12.71 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.25), residues: 1065 helix: -0.77 (0.24), residues: 507 sheet: -1.11 (0.56), residues: 79 loop : -3.90 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 637 TYR 0.011 0.001 TYR B 473 PHE 0.016 0.002 PHE A 467 TRP 0.015 0.001 TRP A 265 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 ( 9261) covalent geometry : angle 0.71584 / 0.35 (12712) SS BOND : bond 0.00234 / 0.15 ( 13) SS BOND : angle 2.27313 / 1.39 ( 26) hydrogen bonds : bond 0.04633 / 3.22 ( 264) hydrogen bonds : angle 4.13936 / 2.89 ( 759) Misc. bond : bond 0.00067 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7104 (mp0) REVERT: A 304 MET cc_start: 0.5883 (mmp) cc_final: 0.5421 (mmt) REVERT: B 126 LEU cc_start: 0.7917 (tp) cc_final: 0.7616 (tt) REVERT: B 304 MET cc_start: 0.7958 (tpp) cc_final: 0.7727 (tpp) REVERT: B 429 LEU cc_start: 0.8470 (tt) cc_final: 0.8075 (tp) REVERT: B 508 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8042 (mmtt) REVERT: B 528 ARG cc_start: 0.8282 (mtm180) cc_final: 0.7903 (mtm110) REVERT: B 575 ILE cc_start: 0.8485 (mt) cc_final: 0.8280 (mt) outliers start: 16 outliers final: 12 residues processed: 107 average time/residue: 0.1110 time to fit residues: 16.1860 Evaluate side-chains 106 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 538 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 13 optimal weight: 0.0770 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.146016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.112176 restraints weight = 14983.433| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.79 r_work: 0.3153 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9277 Z= 0.133 Angle : 0.683 8.085 12738 Z= 0.339 Chirality : 0.041 0.185 1514 Planarity : 0.006 0.089 1448 Dihedral : 12.516 113.707 1462 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.62 % Favored : 85.63 % Rotamer: Outliers : 2.00 % Allowed : 13.53 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.25), residues: 1065 helix: -0.63 (0.24), residues: 508 sheet: -1.19 (0.56), residues: 79 loop : -3.88 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 637 TYR 0.009 0.001 TYR B 473 PHE 0.014 0.001 PHE A 467 TRP 0.013 0.001 TRP A 265 HIS 0.006 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 9261) covalent geometry : angle 0.67736 / 0.34 (12712) SS BOND : bond 0.00257 / 0.18 ( 13) SS BOND : angle 2.03331 / 1.26 ( 26) hydrogen bonds : bond 0.04195 / 2.92 ( 264) hydrogen bonds : angle 3.96232 / 2.77 ( 759) Misc. bond : bond 0.00061 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.6185 (mmp) cc_final: 0.5379 (mmt) REVERT: A 572 MET cc_start: 0.8994 (ppp) cc_final: 0.8312 (ptt) REVERT: B 126 LEU cc_start: 0.7930 (tp) cc_final: 0.7592 (tt) REVERT: B 156 TRP cc_start: 0.7408 (m100) cc_final: 0.7186 (m100) REVERT: B 193 GLN cc_start: 0.6837 (mt0) cc_final: 0.6232 (mm-40) REVERT: B 305 LYS cc_start: 0.7736 (ttmt) cc_final: 0.7530 (tttt) REVERT: B 429 LEU cc_start: 0.8426 (tt) cc_final: 0.8031 (tp) REVERT: B 508 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8153 (mmtt) REVERT: B 528 ARG cc_start: 0.8165 (mtm180) cc_final: 0.7797 (mtm110) REVERT: B 556 ILE cc_start: 0.6449 (OUTLIER) cc_final: 0.5940 (mt) outliers start: 17 outliers final: 10 residues processed: 107 average time/residue: 0.0985 time to fit residues: 14.7499 Evaluate side-chains 100 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 0.0670 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 85 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.146269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113405 restraints weight = 15010.368| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.89 r_work: 0.3175 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9277 Z= 0.130 Angle : 0.673 7.726 12738 Z= 0.337 Chirality : 0.041 0.181 1514 Planarity : 0.006 0.079 1448 Dihedral : 12.153 113.900 1462 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.71 % Favored : 85.54 % Rotamer: Outliers : 2.47 % Allowed : 13.65 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.25), residues: 1065 helix: -0.45 (0.24), residues: 506 sheet: -1.26 (0.55), residues: 81 loop : -3.82 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 637 TYR 0.008 0.001 TYR B 473 PHE 0.013 0.001 PHE A 467 TRP 0.013 0.001 TRP A 265 HIS 0.006 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 9261) covalent geometry : angle 0.66752 / 0.33 (12712) SS BOND : bond 0.00231 / 0.15 ( 13) SS BOND : angle 2.02462 / 1.24 ( 26) hydrogen bonds : bond 0.04025 / 2.78 ( 264) hydrogen bonds : angle 3.88113 / 2.71 ( 759) Misc. bond : bond 0.00057 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.6279 (mmp) cc_final: 0.5901 (mmt) REVERT: A 572 MET cc_start: 0.8995 (ppp) cc_final: 0.8302 (ptt) REVERT: B 126 LEU cc_start: 0.7899 (tp) cc_final: 0.7593 (tt) REVERT: B 429 LEU cc_start: 0.8356 (tt) cc_final: 0.7983 (tp) REVERT: B 508 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8129 (mmtt) REVERT: B 528 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7804 (mtm110) outliers start: 21 outliers final: 14 residues processed: 108 average time/residue: 0.0996 time to fit residues: 15.0208 Evaluate side-chains 103 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 548 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 0.0000 chunk 76 optimal weight: 6.9990 chunk 92 optimal weight: 0.0030 chunk 90 optimal weight: 0.9980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.147120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.113770 restraints weight = 15047.153| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.80 r_work: 0.3125 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9277 Z= 0.123 Angle : 0.693 20.427 12738 Z= 0.339 Chirality : 0.040 0.179 1514 Planarity : 0.006 0.121 1448 Dihedral : 11.845 113.926 1462 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.52 % Favored : 85.73 % Rotamer: Outliers : 2.35 % Allowed : 13.53 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.26), residues: 1065 helix: -0.25 (0.24), residues: 506 sheet: -1.19 (0.55), residues: 81 loop : -3.83 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 637 TYR 0.007 0.001 TYR B 473 PHE 0.012 0.001 PHE A 467 TRP 0.047 0.001 TRP B 156 HIS 0.007 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 9261) covalent geometry : angle 0.68786 / 0.34 (12712) SS BOND : bond 0.00225 / 0.15 ( 13) SS BOND : angle 2.00422 / 1.23 ( 26) hydrogen bonds : bond 0.03772 / 2.62 ( 264) hydrogen bonds : angle 3.81302 / 2.65 ( 759) Misc. bond : bond 0.00050 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.6443 (mmp) cc_final: 0.6138 (mmt) REVERT: A 572 MET cc_start: 0.9040 (ppp) cc_final: 0.8353 (ptt) REVERT: B 126 LEU cc_start: 0.7905 (tp) cc_final: 0.7571 (tt) REVERT: B 429 LEU cc_start: 0.8400 (tt) cc_final: 0.8055 (tp) REVERT: B 508 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8245 (mmtt) REVERT: B 528 ARG cc_start: 0.8172 (mtm180) cc_final: 0.7840 (mtm110) REVERT: B 556 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.6125 (mt) outliers start: 20 outliers final: 16 residues processed: 99 average time/residue: 0.0885 time to fit residues: 12.4070 Evaluate side-chains 100 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 0.0000 chunk 86 optimal weight: 0.1980 chunk 83 optimal weight: 0.5980 chunk 8 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 25 optimal weight: 8.9990 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.147848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.115865 restraints weight = 14901.112| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.98 r_work: 0.3207 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9277 Z= 0.115 Angle : 0.652 14.032 12738 Z= 0.323 Chirality : 0.040 0.177 1514 Planarity : 0.006 0.116 1448 Dihedral : 11.359 113.798 1462 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.43 % Favored : 85.82 % Rotamer: Outliers : 2.12 % Allowed : 13.76 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.26), residues: 1065 helix: -0.04 (0.24), residues: 505 sheet: -1.05 (0.57), residues: 79 loop : -3.85 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 637 TYR 0.006 0.001 TYR A 269 PHE 0.011 0.001 PHE A 423 TRP 0.028 0.001 TRP B 156 HIS 0.006 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 9261) covalent geometry : angle 0.64702 / 0.32 (12712) SS BOND : bond 0.00229 / 0.15 ( 13) SS BOND : angle 1.96502 / 1.20 ( 26) hydrogen bonds : bond 0.03472 / 2.39 ( 264) hydrogen bonds : angle 3.73408 / 2.59 ( 759) Misc. bond : bond 0.00044 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.6280 (mmp) cc_final: 0.6015 (mmt) REVERT: A 566 ASP cc_start: 0.7165 (m-30) cc_final: 0.6926 (t0) REVERT: A 572 MET cc_start: 0.8987 (ppp) cc_final: 0.8281 (ptt) REVERT: B 126 LEU cc_start: 0.7801 (tp) cc_final: 0.7495 (tt) REVERT: B 193 GLN cc_start: 0.6624 (mt0) cc_final: 0.6153 (mm-40) REVERT: B 429 LEU cc_start: 0.8309 (tt) cc_final: 0.7989 (tp) REVERT: B 508 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8189 (mmtt) REVERT: B 528 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7665 (mtm110) REVERT: B 556 ILE cc_start: 0.6374 (OUTLIER) cc_final: 0.6034 (mt) outliers start: 18 outliers final: 16 residues processed: 99 average time/residue: 0.0899 time to fit residues: 12.6242 Evaluate side-chains 102 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 0.0980 chunk 11 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 chunk 40 optimal weight: 0.0970 chunk 46 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 107 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 70 optimal weight: 6.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.148085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.114719 restraints weight = 14871.446| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.82 r_work: 0.3159 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9277 Z= 0.113 Angle : 0.645 14.888 12738 Z= 0.318 Chirality : 0.039 0.177 1514 Planarity : 0.006 0.121 1448 Dihedral : 10.972 113.813 1462 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.15 % Favored : 86.10 % Rotamer: Outliers : 2.24 % Allowed : 13.76 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.26), residues: 1065 helix: 0.12 (0.24), residues: 510 sheet: -0.88 (0.58), residues: 81 loop : -3.83 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 637 TYR 0.007 0.001 TYR B 473 PHE 0.012 0.001 PHE A 467 TRP 0.025 0.001 TRP B 156 HIS 0.006 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 9261) covalent geometry : angle 0.64022 / 0.32 (12712) SS BOND : bond 0.00234 / 0.15 ( 13) SS BOND : angle 1.91670 / 1.17 ( 26) hydrogen bonds : bond 0.03485 / 2.40 ( 264) hydrogen bonds : angle 3.67006 / 2.54 ( 759) Misc. bond : bond 0.00045 / 0.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.6444 (mmp) cc_final: 0.6191 (mmt) REVERT: A 566 ASP cc_start: 0.7273 (m-30) cc_final: 0.7032 (t0) REVERT: A 572 MET cc_start: 0.9018 (ppp) cc_final: 0.8312 (ptt) REVERT: B 126 LEU cc_start: 0.7810 (tp) cc_final: 0.7505 (tt) REVERT: B 193 GLN cc_start: 0.6523 (mt0) cc_final: 0.6183 (mm-40) REVERT: B 365 PRO cc_start: 0.3696 (Cg_exo) cc_final: 0.3418 (Cg_endo) REVERT: B 429 LEU cc_start: 0.8341 (tt) cc_final: 0.8030 (tp) REVERT: B 508 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8226 (mmtt) REVERT: B 556 ILE cc_start: 0.6405 (OUTLIER) cc_final: 0.6018 (mt) outliers start: 19 outliers final: 17 residues processed: 96 average time/residue: 0.0880 time to fit residues: 12.1475 Evaluate side-chains 102 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 90 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 77 optimal weight: 6.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.148027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.114336 restraints weight = 14791.738| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.76 r_work: 0.3177 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9277 Z= 0.117 Angle : 0.684 23.190 12738 Z= 0.330 Chirality : 0.039 0.177 1514 Planarity : 0.006 0.124 1448 Dihedral : 10.828 113.859 1462 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.66 % Allowed : 13.43 % Favored : 85.92 % Rotamer: Outliers : 2.35 % Allowed : 14.59 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.26), residues: 1065 helix: 0.25 (0.24), residues: 511 sheet: -0.83 (0.59), residues: 81 loop : -3.81 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 637 TYR 0.007 0.001 TYR B 473 PHE 0.010 0.001 PHE B 467 TRP 0.024 0.001 TRP B 156 HIS 0.007 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9261) covalent geometry : angle 0.67957 / 0.33 (12712) SS BOND : bond 0.00229 / 0.15 ( 13) SS BOND : angle 1.86836 / 1.13 ( 26) hydrogen bonds : bond 0.03538 / 2.44 ( 264) hydrogen bonds : angle 3.67806 / 2.54 ( 759) Misc. bond : bond 0.00046 / 0.02 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2087.27 seconds wall clock time: 36 minutes 29.85 seconds (2189.85 seconds total)