Starting phenix.real_space_refine on Sun Feb 8 07:27:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0p_48789/02_2026/9n0p_48789.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0p_48789/02_2026/9n0p_48789.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/9n0p_48789/02_2026/9n0p_48789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0p_48789/02_2026/9n0p_48789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n0p_48789/02_2026/9n0p_48789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0p_48789/02_2026/9n0p_48789.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= 0.000 sd= 0.014 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 S 76 5.16 5 C 13299 2.51 5 N 3703 2.21 5 O 3839 1.98 5 H 20509 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41426 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 8655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8655 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 22, 'TRANS': 525} Chain breaks: 1 Chain: "C" Number of atoms: 8581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 8581 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 22, 'TRANS': 521} Chain breaks: 2 Chain: "A" Number of atoms: 12126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 12126 Classifications: {'peptide': 766} Link IDs: {'PTRANS': 28, 'TRANS': 737} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 12064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 12064 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 28, 'TRANS': 735} Chain breaks: 4 Time building chain proxies: 8.15, per 1000 atoms: 0.20 Number of scatterers: 41426 At special positions: 0 Unit cell: (151.2, 144.72, 103.68, 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 76 16.00 O 3839 8.00 N 3703 7.00 C 13299 6.00 H 20509 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.2 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5010 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 23 sheets defined 56.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'B' and resid 360 through 369 Processing helix chain 'B' and resid 379 through 392 removed outlier: 3.565A pdb=" N ALA B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 removed outlier: 3.819A pdb=" N HIS B 409 " --> pdb=" O HIS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 removed outlier: 3.743A pdb=" N GLU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 451 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 473 through 482 Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.560A pdb=" N THR B 501 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 4.317A pdb=" N GLN B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 removed outlier: 3.570A pdb=" N SER B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 539 Processing helix chain 'B' and resid 542 through 548 removed outlier: 4.130A pdb=" N VAL B 547 " --> pdb=" O SER B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 572 removed outlier: 3.643A pdb=" N LEU B 572 " --> pdb=" O HIS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 592 through 604 removed outlier: 3.707A pdb=" N GLY B 597 " --> pdb=" O ARG B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 648 removed outlier: 4.084A pdb=" N SER B 615 " --> pdb=" O GLN B 611 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN B 622 " --> pdb=" O LEU B 618 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 625 " --> pdb=" O ARG B 621 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG B 632 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 646 " --> pdb=" O ARG B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 655 removed outlier: 4.409A pdb=" N TRP B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 665 through 669 Processing helix chain 'B' and resid 683 through 694 Processing helix chain 'B' and resid 708 through 711 Processing helix chain 'B' and resid 713 through 721 removed outlier: 3.553A pdb=" N PHE B 717 " --> pdb=" O ASN B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 772 removed outlier: 3.614A pdb=" N VAL B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.520A pdb=" N ILE B 787 " --> pdb=" O HIS B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 Processing helix chain 'B' and resid 814 through 822 removed outlier: 3.644A pdb=" N ALA B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 842 removed outlier: 3.578A pdb=" N ARG B 838 " --> pdb=" O GLY B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 879 Processing helix chain 'B' and resid 897 through 917 removed outlier: 3.581A pdb=" N GLY B 915 " --> pdb=" O VAL B 911 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 916 " --> pdb=" O ALA B 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.742A pdb=" N ALA C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 416 removed outlier: 3.859A pdb=" N HIS C 409 " --> pdb=" O HIS C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 452 removed outlier: 3.590A pdb=" N GLU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 451 " --> pdb=" O ASP C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 473 through 483 removed outlier: 3.526A pdb=" N ALA C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 498 removed outlier: 4.105A pdb=" N ALA C 498 " --> pdb=" O ALA C 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 503 through 508 removed outlier: 4.029A pdb=" N GLN C 508 " --> pdb=" O PRO C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.707A pdb=" N SER C 523 " --> pdb=" O GLU C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 538 Processing helix chain 'C' and resid 542 through 549 removed outlier: 3.969A pdb=" N VAL C 547 " --> pdb=" O SER C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 571 removed outlier: 3.580A pdb=" N LYS C 570 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER C 571 " --> pdb=" O THR C 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 567 through 571' Processing helix chain 'C' and resid 587 through 592 Processing helix chain 'C' and resid 592 through 604 Processing helix chain 'C' and resid 609 through 626 removed outlier: 3.617A pdb=" N SER C 615 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP C 617 " --> pdb=" O LEU C 613 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 648 removed outlier: 3.767A pdb=" N LEU C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 654 Processing helix chain 'C' and resid 659 through 664 Processing helix chain 'C' and resid 665 through 669 Processing helix chain 'C' and resid 684 through 694 Processing helix chain 'C' and resid 713 through 721 Processing helix chain 'C' and resid 747 through 772 Processing helix chain 'C' and resid 773 through 789 removed outlier: 3.562A pdb=" N ILE C 787 " --> pdb=" O HIS C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 Processing helix chain 'C' and resid 814 through 822 removed outlier: 3.564A pdb=" N ALA C 818 " --> pdb=" O ASP C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 842 Processing helix chain 'C' and resid 869 through 877 Processing helix chain 'C' and resid 897 through 915 removed outlier: 3.813A pdb=" N GLY C 915 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 46 removed outlier: 3.968A pdb=" N ALA A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 removed outlier: 3.877A pdb=" N ALA A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 89 Processing helix chain 'A' and resid 90 through 108 removed outlier: 3.649A pdb=" N GLU A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 removed outlier: 3.534A pdb=" N THR A 112 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.708A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.513A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 239 Processing helix chain 'A' and resid 275 through 288 removed outlier: 4.100A pdb=" N THR A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 368 Processing helix chain 'A' and resid 379 through 392 Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.790A pdb=" N HIS A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 452 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.573A pdb=" N ALA A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 4.026A pdb=" N PHE A 499 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 510 through 523 Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'A' and resid 542 through 548 removed outlier: 4.258A pdb=" N VAL A 547 " --> pdb=" O SER A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 592 through 604 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.582A pdb=" N ALA A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 610 through 615' Processing helix chain 'A' and resid 616 through 624 removed outlier: 3.773A pdb=" N VAL A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 624 " --> pdb=" O ARG A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 648 Processing helix chain 'A' and resid 648 through 655 removed outlier: 4.082A pdb=" N TRP A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 711 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 747 through 772 removed outlier: 3.701A pdb=" N ALA A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 787 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 832 through 843 removed outlier: 4.278A pdb=" N GLY A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG A 838 " --> pdb=" O GLY A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 879 Processing helix chain 'A' and resid 897 through 916 Processing helix chain 'D' and resid 23 through 47 removed outlier: 3.824A pdb=" N ALA D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY D 47 " --> pdb=" O VAL D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 90 through 109 removed outlier: 3.609A pdb=" N GLU D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 151 through 158 Processing helix chain 'D' and resid 175 through 186 removed outlier: 3.603A pdb=" N LEU D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.624A pdb=" N TYR D 288 " --> pdb=" O LEU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 379 through 392 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.763A pdb=" N HIS D 409 " --> pdb=" O HIS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 452 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 473 through 485 removed outlier: 3.707A pdb=" N ALA D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 484 " --> pdb=" O GLU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 503 removed outlier: 3.829A pdb=" N ALA D 500 " --> pdb=" O TYR D 497 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR D 501 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL D 503 " --> pdb=" O ALA D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 509 Processing helix chain 'D' and resid 510 through 523 Processing helix chain 'D' and resid 524 through 538 Processing helix chain 'D' and resid 542 through 548 removed outlier: 4.192A pdb=" N VAL D 547 " --> pdb=" O SER D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 607 through 626 removed outlier: 4.398A pdb=" N GLN D 611 " --> pdb=" O SER D 607 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU D 613 " --> pdb=" O ASN D 609 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA D 614 " --> pdb=" O GLN D 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D 618 " --> pdb=" O ALA D 614 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA D 619 " --> pdb=" O SER D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 648 Processing helix chain 'D' and resid 648 through 655 removed outlier: 3.902A pdb=" N TRP D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 721 Processing helix chain 'D' and resid 721 through 726 removed outlier: 3.984A pdb=" N ARG D 725 " --> pdb=" O ILE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 772 Processing helix chain 'D' and resid 773 through 787 removed outlier: 3.563A pdb=" N ILE D 787 " --> pdb=" O HIS D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 801 through 805 removed outlier: 3.749A pdb=" N ARG D 805 " --> pdb=" O LEU D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 822 Processing helix chain 'D' and resid 832 through 843 removed outlier: 4.289A pdb=" N GLY D 837 " --> pdb=" O ILE D 833 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ARG D 838 " --> pdb=" O GLY D 834 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 843 " --> pdb=" O ARG D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 879 Processing helix chain 'D' and resid 897 through 917 Processing sheet with id=AA1, first strand: chain 'B' and resid 372 through 376 removed outlier: 7.647A pdb=" N LEU B 491 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 460 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP B 493 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU B 462 " --> pdb=" O ASP B 493 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE B 397 " --> pdb=" O MET B 459 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU B 461 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 399 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N THR B 463 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ASP B 401 " --> pdb=" O THR B 463 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 398 " --> pdb=" O MET B 420 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 422 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 400 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 426 through 427 Processing sheet with id=AA3, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.561A pdb=" N VAL B 697 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 656 through 657 removed outlier: 3.763A pdb=" N ARG B 656 " --> pdb=" O PHE B 706 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 737 " --> pdb=" O SER B 734 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 732 " --> pdb=" O LEU B 739 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 828 through 831 Processing sheet with id=AA6, first strand: chain 'C' and resid 372 through 376 Processing sheet with id=AA7, first strand: chain 'C' and resid 398 through 401 removed outlier: 6.285A pdb=" N VAL C 398 " --> pdb=" O MET C 420 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU C 422 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE C 400 " --> pdb=" O LEU C 422 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 426 through 427 Processing sheet with id=AA9, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.622A pdb=" N VAL C 697 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 656 through 657 Processing sheet with id=AB2, first strand: chain 'C' and resid 828 through 831 Processing sheet with id=AB3, first strand: chain 'C' and resid 853 through 854 removed outlier: 3.570A pdb=" N HIS C 885 " --> pdb=" O VAL C 853 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 166 through 173 removed outlier: 6.720A pdb=" N GLN A 134 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLU A 169 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR A 136 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU A 171 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL A 138 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL A 173 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU A 140 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N PHE A 135 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N ALA A 191 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A 137 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ILE A 193 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 139 " --> pdb=" O ILE A 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 372 through 376 removed outlier: 3.607A pdb=" N PHE A 490 " --> pdb=" O ARG A 561 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 565 " --> pdb=" O TRP A 492 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 418 through 422 removed outlier: 6.295A pdb=" N VAL A 398 " --> pdb=" O MET A 420 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 422 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 400 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 397 " --> pdb=" O MET A 459 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU A 461 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A 399 " --> pdb=" O LEU A 461 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB8, first strand: chain 'A' and resid 656 through 657 removed outlier: 4.059A pdb=" N LYS A 732 " --> pdb=" O LEU A 739 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 828 through 831 Processing sheet with id=AC1, first strand: chain 'D' and resid 168 through 173 removed outlier: 3.588A pdb=" N GLU D 169 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR D 137 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 191 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP D 243 " --> pdb=" O GLN D 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 372 through 376 removed outlier: 3.738A pdb=" N MET D 580 " --> pdb=" O HIS D 566 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS D 566 " --> pdb=" O MET D 580 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D 565 " --> pdb=" O TRP D 492 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU D 460 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP D 493 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET D 459 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL D 398 " --> pdb=" O MET D 420 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU D 422 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE D 400 " --> pdb=" O LEU D 422 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 702 through 706 removed outlier: 4.328A pdb=" N LYS D 732 " --> pdb=" O LEU D 739 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 828 through 831 Processing sheet with id=AC5, first strand: chain 'D' and resid 853 through 854 1025 hydrogen bonds defined for protein. 2874 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: 11.11 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 20487 1.00 - 1.21: 22 1.21 - 1.41: 9043 1.41 - 1.61: 12210 1.61 - 1.82: 130 Bond restraints: 41892 Sorted by residual: bond pdb=" NE2 GLN C 866 " pdb="HE22 GLN C 866 " ideal model delta sigma weight residual 0.860 0.801 0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" ND2 ASN B 464 " pdb="HD22 ASN B 464 " ideal model delta sigma weight residual 0.860 0.805 0.055 2.00e-02 2.50e+03 7.66e+00 bond pdb=" NE2 GLN C 611 " pdb="HE22 GLN C 611 " ideal model delta sigma weight residual 0.860 0.818 0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" NE2 GLN B 611 " pdb="HE22 GLN B 611 " ideal model delta sigma weight residual 0.860 0.818 0.042 2.00e-02 2.50e+03 4.37e+00 bond pdb=" NE2 GLN B 789 " pdb="HE22 GLN B 789 " ideal model delta sigma weight residual 0.860 0.819 0.041 2.00e-02 2.50e+03 4.25e+00 ... (remaining 41887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.18: 75335 7.18 - 14.36: 3 14.36 - 21.54: 8 21.54 - 28.72: 14 28.72 - 35.90: 11 Bond angle restraints: 75371 Sorted by residual: angle pdb=" CG ASN A 286 " pdb=" ND2 ASN A 286 " pdb="HD22 ASN A 286 " ideal model delta sigma weight residual 120.00 155.90 -35.90 3.00e+00 1.11e-01 1.43e+02 angle pdb=" CD GLN C 610 " pdb=" NE2 GLN C 610 " pdb="HE22 GLN C 610 " ideal model delta sigma weight residual 120.00 155.86 -35.86 3.00e+00 1.11e-01 1.43e+02 angle pdb=" CG ASN B 609 " pdb=" ND2 ASN B 609 " pdb="HD22 ASN B 609 " ideal model delta sigma weight residual 120.00 153.58 -33.58 3.00e+00 1.11e-01 1.25e+02 angle pdb="HD21 ASN A 286 " pdb=" ND2 ASN A 286 " pdb="HD22 ASN A 286 " ideal model delta sigma weight residual 120.00 88.33 31.67 3.00e+00 1.11e-01 1.11e+02 angle pdb="HE21 GLN C 610 " pdb=" NE2 GLN C 610 " pdb="HE22 GLN C 610 " ideal model delta sigma weight residual 120.00 88.67 31.33 3.00e+00 1.11e-01 1.09e+02 ... (remaining 75366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 17442 17.97 - 35.94: 1589 35.94 - 53.91: 502 53.91 - 71.88: 126 71.88 - 89.85: 60 Dihedral angle restraints: 19719 sinusoidal: 10565 harmonic: 9154 Sorted by residual: dihedral pdb=" CA TYR C 855 " pdb=" C TYR C 855 " pdb=" N PRO C 856 " pdb=" CA PRO C 856 " ideal model delta harmonic sigma weight residual 180.00 153.40 26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA TYR A 855 " pdb=" C TYR A 855 " pdb=" N PRO A 856 " pdb=" CA PRO A 856 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ILE D 721 " pdb=" C ILE D 721 " pdb=" N LEU D 722 " pdb=" CA LEU D 722 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 19716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2455 0.039 - 0.079: 594 0.079 - 0.118: 197 0.118 - 0.157: 24 0.157 - 0.197: 1 Chirality restraints: 3271 Sorted by residual: chirality pdb=" CG LEU B 879 " pdb=" CB LEU B 879 " pdb=" CD1 LEU B 879 " pdb=" CD2 LEU B 879 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CB VAL B 631 " pdb=" CA VAL B 631 " pdb=" CG1 VAL B 631 " pdb=" CG2 VAL B 631 " both_signs ideal model delta sigma weight residual False -2.63 -2.79 0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE D 730 " pdb=" N ILE D 730 " pdb=" C ILE D 730 " pdb=" CB ILE D 730 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 3268 not shown) Planarity restraints: 6261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 611 " 0.046 2.00e-02 2.50e+03 9.92e-02 1.48e+02 pdb=" CD GLN C 611 " -0.117 2.00e-02 2.50e+03 pdb=" OE1 GLN C 611 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN C 611 " 0.164 2.00e-02 2.50e+03 pdb="HE21 GLN C 611 " 0.038 2.00e-02 2.50e+03 pdb="HE22 GLN C 611 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 611 " -0.046 2.00e-02 2.50e+03 9.92e-02 1.48e+02 pdb=" CD GLN B 611 " 0.119 2.00e-02 2.50e+03 pdb=" OE1 GLN B 611 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN B 611 " -0.163 2.00e-02 2.50e+03 pdb="HE21 GLN B 611 " -0.040 2.00e-02 2.50e+03 pdb="HE22 GLN B 611 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 789 " -0.042 2.00e-02 2.50e+03 9.79e-02 1.44e+02 pdb=" CD GLN B 789 " 0.115 2.00e-02 2.50e+03 pdb=" OE1 GLN B 789 " 0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN B 789 " -0.162 2.00e-02 2.50e+03 pdb="HE21 GLN B 789 " -0.042 2.00e-02 2.50e+03 pdb="HE22 GLN B 789 " 0.121 2.00e-02 2.50e+03 ... (remaining 6258 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 2244 2.18 - 2.79: 83550 2.79 - 3.39: 117575 3.39 - 4.00: 151469 4.00 - 4.60: 235296 Nonbonded interactions: 590134 Sorted by model distance: nonbonded pdb=" HZ1 LYS C 647 " pdb=" OD2 ASP A 116 " model vdw 1.579 2.450 nonbonded pdb="HH21 ARG B 642 " pdb=" O LEU B 658 " model vdw 1.618 2.450 nonbonded pdb=" OE1 GLU A 123 " pdb=" H GLU A 123 " model vdw 1.618 2.450 nonbonded pdb=" O ASP C 827 " pdb=" HG1 THR C 897 " model vdw 1.620 2.450 nonbonded pdb=" O ASP B 827 " pdb=" HG1 THR B 897 " model vdw 1.632 2.450 ... (remaining 590129 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 23 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2 or name H or name HA \ )) or resid 117 through 196 or resid 228 through 240 or resid 264 or resid 268 \ or resid 270 or resid 273 through 387 or (resid 388 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2 or name H or name HA )) or res \ id 389 through 391 or (resid 392 and (name N or name CA or name C or name O or n \ ame CB or name OG1 or name CG2 or name H or name HA )) or resid 393 through 712 \ or (resid 713 and (name N or name CA or name C or name O or name CB or name CG o \ r name OD1 or name ND2 or name H or name HA )) or resid 714 or (resid 715 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2 or name CE1 or name CE2 or name CZ or name OH or name H or name HA )) or resi \ d 716 through 746 or (resid 747 and (name N or name CA or name C or name O or na \ me CB or name OG1 or name CG2 or name H or name HA )) or resid 748 through 749 o \ r (resid 750 and (name N or name CA or name C or name O or name CB or name OG or \ name H or name HA )) or resid 751 through 752 or (resid 753 and (name N or name \ CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE \ 1 or name CE2 or name CZ or name OH or name H or name HA )) or (resid 754 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2 or name H or name HA )) or resid 755 through 917)) selection = (chain 'D' and (resid 23 through 145 or resid 150 through 240 or resid 243 or re \ sid 245 or resid 247 or resid 273 through 287 or (resid 288 and (name N or name \ CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 \ or name CE2 or name CZ or name OH or name H or name HA )) or resid 289 through \ 298 or (resid 358 and (name N or name CA or name C or name O or name CB or name \ H or name HA or name HB2 or name HB3)) or resid 359 through 565 or (resid 566 an \ d (name N or name CA or name C or name O or name CB or name CG or name ND1 or na \ me CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or n \ ame HD2 or name HE1 or name HE2)) or resid 567 through 610 or (resid 611 and (na \ me N or name CA or name C or name O or name CB or name H or name HA or name HB2 \ or name HB3)) or resid 612 through 670 or resid 692 through 917)) } ncs_group { reference = (chain 'B' and (resid 360 through 493 or (resid 494 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name \ H or name HA )) or resid 495 through 565 or (resid 566 and (name N or name CA or \ name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or n \ ame NE2 or name H or name HA )) or resid 567 through 571 or resid 577 through 67 \ 0 or resid 683 through 796 or (resid 797 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ or name H or name HA )) or (resid 798 and (name N or name CA or name C or n \ ame O or name CB or name OG or name H or name HA )) or (resid 799 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e OE2 or name H or name HA )) or resid 800 through 822 or (resid 823 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ or name OH or name H or name HA )) or resid 824 \ through 866 or (resid 867 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name H or name HA )) or resid 868 through \ 917)) selection = (chain 'C' and (resid 360 through 646 or (resid 647 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA )) or resid 648 through 917)) } 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: 11.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.260 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 41.260 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.003 0.063 21383 Z= 0.131 Angle : 0.586 13.422 29065 Z= 0.312 Chirality : 0.039 0.197 3271 Planarity : 0.005 0.080 3754 Dihedral : 16.540 89.725 7750 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.18 % Allowed : 20.72 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2590 helix: 1.55 (0.15), residues: 1247 sheet: -1.80 (0.28), residues: 313 loop : -1.02 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 725 TYR 0.019 0.001 TYR D 497 PHE 0.034 0.001 PHE A 804 TRP 0.014 0.001 TRP C 368 HIS 0.009 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00299 (21383) covalent geometry : angle 0.58638 (29065) hydrogen bonds : bond 0.17245 ( 1025) hydrogen bonds : angle 6.66637 ( 2874) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 560 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue TYR 823 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue VAL 262 is missing expected H atoms. Skipping. Residue TYR 288 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue THR 392 is missing expected H atoms. Skipping. Residue TYR 715 is missing expected H atoms. Skipping. Residue THR 747 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue TYR 753 is missing expected H atoms. Skipping. Residue LEU 754 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 249 time to evaluate : 1.150 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 outliers start: 4 outliers final: 2 residues processed: 251 average time/residue: 0.4230 time to fit residues: 155.9026 Evaluate side-chains 249 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 741 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 258 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 586 GLN A 622 GLN D 464 ASN ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.165356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132361 restraints weight = 82527.581| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.48 r_work: 0.3574 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21383 Z= 0.180 Angle : 0.561 8.516 29065 Z= 0.300 Chirality : 0.040 0.159 3271 Planarity : 0.005 0.054 3754 Dihedral : 4.614 37.226 2925 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.91 % Allowed : 17.81 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2590 helix: 1.42 (0.15), residues: 1293 sheet: -1.98 (0.28), residues: 312 loop : -1.08 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 759 TYR 0.019 0.002 TYR A 635 PHE 0.016 0.002 PHE A 804 TRP 0.014 0.001 TRP B 687 HIS 0.007 0.001 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00411 (21383) covalent geometry : angle 0.56052 (29065) hydrogen bonds : bond 0.04413 ( 1025) hydrogen bonds : angle 5.13734 ( 2874) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 560 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue TYR 823 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue VAL 262 is missing expected H atoms. Skipping. Residue TYR 288 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue THR 392 is missing expected H atoms. Skipping. Residue TYR 715 is missing expected H atoms. Skipping. Residue THR 747 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue TYR 753 is missing expected H atoms. Skipping. Residue LEU 754 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 0.998 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: B 392 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8744 (p) REVERT: A 577 GLN cc_start: 0.7227 (mp10) cc_final: 0.6992 (mp10) REVERT: D 507 ARG cc_start: 0.6428 (mtm180) cc_final: 0.6225 (mtp180) outliers start: 42 outliers final: 24 residues processed: 293 average time/residue: 0.3990 time to fit residues: 171.8154 Evaluate side-chains 271 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 246 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 704 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 213 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 ASN A 622 GLN ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.161335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128560 restraints weight = 82893.516| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.44 r_work: 0.3516 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 21383 Z= 0.248 Angle : 0.599 6.395 29065 Z= 0.325 Chirality : 0.041 0.161 3271 Planarity : 0.005 0.055 3754 Dihedral : 4.891 30.024 2923 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.60 % Allowed : 17.76 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2590 helix: 1.02 (0.14), residues: 1294 sheet: -2.04 (0.28), residues: 295 loop : -1.50 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 517 TYR 0.028 0.002 TYR A 288 PHE 0.019 0.002 PHE B 742 TRP 0.018 0.002 TRP B 687 HIS 0.009 0.001 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00578 (21383) covalent geometry : angle 0.59913 (29065) hydrogen bonds : bond 0.04715 ( 1025) hydrogen bonds : angle 5.07680 ( 2874) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 560 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue TYR 823 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue VAL 262 is missing expected H atoms. Skipping. Residue TYR 288 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue THR 392 is missing expected H atoms. Skipping. Residue TYR 715 is missing expected H atoms. Skipping. Residue THR 747 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue TYR 753 is missing expected H atoms. Skipping. Residue LEU 754 is missing expected H atoms. Skipping. Evaluate side-chains 314 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 257 time to evaluate : 1.015 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: B 392 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8671 (p) REVERT: B 530 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: C 855 TYR cc_start: 0.7269 (t80) cc_final: 0.7043 (t80) REVERT: A 124 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: A 288 TYR cc_start: 0.6574 (t80) cc_final: 0.6229 (t80) REVERT: A 507 ARG cc_start: 0.6229 (mtm180) cc_final: 0.6005 (mtp180) REVERT: A 577 GLN cc_start: 0.7229 (mp10) cc_final: 0.6957 (mp10) REVERT: D 507 ARG cc_start: 0.6599 (mtm180) cc_final: 0.6392 (mtp180) outliers start: 57 outliers final: 36 residues processed: 296 average time/residue: 0.4279 time to fit residues: 186.3026 Evaluate side-chains 282 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 893 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 258 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN A 622 GLN ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.165359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132386 restraints weight = 81741.963| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.46 r_work: 0.3569 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21383 Z= 0.111 Angle : 0.495 5.595 29065 Z= 0.263 Chirality : 0.038 0.158 3271 Planarity : 0.004 0.049 3754 Dihedral : 4.532 26.399 2923 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.82 % Allowed : 18.67 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2590 helix: 1.45 (0.15), residues: 1292 sheet: -1.94 (0.28), residues: 306 loop : -1.24 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 621 TYR 0.024 0.001 TYR B 497 PHE 0.009 0.001 PHE B 600 TRP 0.014 0.001 TRP B 687 HIS 0.004 0.001 HIS D 566 Details of bonding type rmsd covalent geometry : bond 0.00253 (21383) covalent geometry : angle 0.49525 (29065) hydrogen bonds : bond 0.03684 ( 1025) hydrogen bonds : angle 4.71300 ( 2874) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 560 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue TYR 823 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue VAL 262 is missing expected H atoms. Skipping. Residue TYR 288 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue THR 392 is missing expected H atoms. Skipping. Residue TYR 715 is missing expected H atoms. Skipping. Residue THR 747 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue TYR 753 is missing expected H atoms. Skipping. Residue LEU 754 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 1.133 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 392 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8758 (p) REVERT: C 855 TYR cc_start: 0.7269 (t80) cc_final: 0.7061 (t80) REVERT: A 124 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: A 288 TYR cc_start: 0.6335 (t80) cc_final: 0.6118 (t80) REVERT: A 577 GLN cc_start: 0.7128 (mp10) cc_final: 0.6833 (mp10) outliers start: 40 outliers final: 30 residues processed: 287 average time/residue: 0.4188 time to fit residues: 177.5375 Evaluate side-chains 275 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 798 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 159 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.160296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128275 restraints weight = 82921.660| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.40 r_work: 0.3510 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21383 Z= 0.249 Angle : 0.586 5.768 29065 Z= 0.317 Chirality : 0.041 0.157 3271 Planarity : 0.005 0.047 3754 Dihedral : 4.883 30.358 2923 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.10 % Allowed : 18.72 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.17), residues: 2590 helix: 0.99 (0.14), residues: 1296 sheet: -1.93 (0.30), residues: 275 loop : -1.55 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 702 TYR 0.026 0.002 TYR B 497 PHE 0.015 0.002 PHE D 135 TRP 0.018 0.002 TRP B 687 HIS 0.007 0.001 HIS D 793 Details of bonding type rmsd covalent geometry : bond 0.00584 (21383) covalent geometry : angle 0.58584 (29065) hydrogen bonds : bond 0.04304 ( 1025) hydrogen bonds : angle 4.90544 ( 2874) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 560 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue TYR 823 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue VAL 262 is missing expected H atoms. Skipping. Residue TYR 288 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue THR 392 is missing expected H atoms. Skipping. Residue TYR 715 is missing expected H atoms. Skipping. Residue THR 747 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue TYR 753 is missing expected H atoms. Skipping. Residue LEU 754 is missing expected H atoms. Skipping. Evaluate side-chains 317 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 249 time to evaluate : 1.069 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 392 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 413 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8176 (t) REVERT: B 530 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: B 633 HIS cc_start: 0.7928 (t-170) cc_final: 0.7359 (m-70) REVERT: C 369 ASN cc_start: 0.7888 (m-40) cc_final: 0.7673 (t0) REVERT: C 703 LEU cc_start: 0.8682 (mp) cc_final: 0.8444 (mt) REVERT: C 723 MET cc_start: 0.5298 (ttm) cc_final: 0.4627 (ptt) REVERT: C 855 TYR cc_start: 0.7342 (t80) cc_final: 0.7136 (t80) REVERT: A 507 ARG cc_start: 0.6191 (mtm180) cc_final: 0.5961 (mtp180) REVERT: A 577 GLN cc_start: 0.7148 (mp10) cc_final: 0.6841 (mp10) REVERT: D 507 ARG cc_start: 0.6629 (mtm180) cc_final: 0.6425 (mtp180) outliers start: 68 outliers final: 47 residues processed: 299 average time/residue: 0.4167 time to fit residues: 183.8563 Evaluate side-chains 292 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 489 CYS Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 728 ILE Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 798 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 220 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 179 optimal weight: 0.0570 chunk 238 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 0.0060 chunk 185 optimal weight: 4.9990 overall best weight: 1.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN D 133 GLN D 464 ASN ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.163517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130759 restraints weight = 82041.121| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.45 r_work: 0.3550 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21383 Z= 0.132 Angle : 0.510 5.702 29065 Z= 0.270 Chirality : 0.038 0.158 3271 Planarity : 0.004 0.051 3754 Dihedral : 4.604 26.824 2923 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.87 % Allowed : 19.40 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2590 helix: 1.38 (0.15), residues: 1283 sheet: -1.90 (0.28), residues: 299 loop : -1.38 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 692 TYR 0.023 0.001 TYR B 497 PHE 0.009 0.001 PHE A 812 TRP 0.015 0.001 TRP B 687 HIS 0.006 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00305 (21383) covalent geometry : angle 0.50959 (29065) hydrogen bonds : bond 0.03641 ( 1025) hydrogen bonds : angle 4.62947 ( 2874) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 560 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue TYR 823 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue VAL 262 is missing expected H atoms. Skipping. Residue TYR 288 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue THR 392 is missing expected H atoms. Skipping. Residue TYR 715 is missing expected H atoms. Skipping. Residue THR 747 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue TYR 753 is missing expected H atoms. Skipping. Residue LEU 754 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 1.175 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 369 ASN cc_start: 0.5016 (t0) cc_final: 0.4745 (t0) REVERT: B 392 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8688 (p) REVERT: C 378 ASN cc_start: 0.7541 (m110) cc_final: 0.6919 (t0) REVERT: C 392 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8687 (p) REVERT: C 723 MET cc_start: 0.5440 (ttm) cc_final: 0.4733 (ptt) REVERT: A 124 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: A 577 GLN cc_start: 0.7078 (mp10) cc_final: 0.6767 (mp10) REVERT: D 433 TYR cc_start: 0.8276 (m-10) cc_final: 0.8030 (m-10) REVERT: D 507 ARG cc_start: 0.6446 (mtm180) cc_final: 0.6244 (mtp180) outliers start: 41 outliers final: 33 residues processed: 286 average time/residue: 0.4270 time to fit residues: 179.0543 Evaluate side-chains 279 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 798 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 150 optimal weight: 0.0270 chunk 187 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN A 622 GLN ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 752 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.162991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130760 restraints weight = 81823.216| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.41 r_work: 0.3550 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21383 Z= 0.140 Angle : 0.508 6.182 29065 Z= 0.269 Chirality : 0.038 0.156 3271 Planarity : 0.004 0.048 3754 Dihedral : 4.547 31.097 2923 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.14 % Allowed : 18.94 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2590 helix: 1.44 (0.15), residues: 1286 sheet: -1.93 (0.28), residues: 299 loop : -1.35 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 517 TYR 0.031 0.001 TYR B 497 PHE 0.010 0.001 PHE D 135 TRP 0.014 0.001 TRP B 687 HIS 0.019 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00324 (21383) covalent geometry : angle 0.50825 (29065) hydrogen bonds : bond 0.03589 ( 1025) hydrogen bonds : angle 4.57448 ( 2874) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 560 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue TYR 823 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue VAL 262 is missing expected H atoms. Skipping. Residue TYR 288 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue THR 392 is missing expected H atoms. Skipping. Residue TYR 715 is missing expected H atoms. Skipping. Residue THR 747 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue TYR 753 is missing expected H atoms. Skipping. Residue LEU 754 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 250 time to evaluate : 1.186 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 369 ASN cc_start: 0.5083 (t0) cc_final: 0.4826 (t0) REVERT: B 392 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8691 (p) REVERT: C 378 ASN cc_start: 0.7538 (m110) cc_final: 0.6964 (t0) REVERT: C 392 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8712 (p) REVERT: C 723 MET cc_start: 0.5422 (ttm) cc_final: 0.4774 (ptt) REVERT: A 124 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7920 (mt0) REVERT: A 577 GLN cc_start: 0.6976 (mp10) cc_final: 0.6661 (mp10) REVERT: D 433 TYR cc_start: 0.8327 (m-10) cc_final: 0.8095 (m-10) REVERT: D 507 ARG cc_start: 0.6455 (mtm180) cc_final: 0.6255 (mtp180) outliers start: 47 outliers final: 40 residues processed: 285 average time/residue: 0.4194 time to fit residues: 177.4241 Evaluate side-chains 283 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 798 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 174 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN ** D 566 HIS ** 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 = 0.4081 r_free = 0.4081 target = 0.163295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131091 restraints weight = 81683.455| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.40 r_work: 0.3553 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21383 Z= 0.139 Angle : 0.506 6.672 29065 Z= 0.267 Chirality : 0.038 0.156 3271 Planarity : 0.004 0.049 3754 Dihedral : 4.505 30.303 2923 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.32 % Allowed : 18.90 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2590 helix: 1.46 (0.15), residues: 1290 sheet: -1.96 (0.28), residues: 300 loop : -1.32 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 517 TYR 0.039 0.001 TYR B 497 PHE 0.009 0.001 PHE A 812 TRP 0.014 0.001 TRP B 687 HIS 0.012 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00324 (21383) covalent geometry : angle 0.50573 (29065) hydrogen bonds : bond 0.03507 ( 1025) hydrogen bonds : angle 4.53112 ( 2874) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 560 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue TYR 823 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue VAL 262 is missing expected H atoms. Skipping. Residue TYR 288 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue THR 392 is missing expected H atoms. Skipping. Residue TYR 715 is missing expected H atoms. Skipping. Residue THR 747 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue TYR 753 is missing expected H atoms. Skipping. Residue LEU 754 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 249 time to evaluate : 1.148 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 369 ASN cc_start: 0.5090 (t0) cc_final: 0.4791 (t0) REVERT: B 392 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8675 (p) REVERT: C 369 ASN cc_start: 0.7869 (m-40) cc_final: 0.7657 (t0) REVERT: C 378 ASN cc_start: 0.7550 (m110) cc_final: 0.7067 (t0) REVERT: C 723 MET cc_start: 0.5333 (ttm) cc_final: 0.4836 (ptt) REVERT: A 124 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: A 577 GLN cc_start: 0.7098 (mp10) cc_final: 0.6782 (mp10) REVERT: A 609 ASN cc_start: 0.7552 (m110) cc_final: 0.6345 (t0) REVERT: D 433 TYR cc_start: 0.8314 (m-10) cc_final: 0.8076 (m-10) outliers start: 51 outliers final: 47 residues processed: 287 average time/residue: 0.4233 time to fit residues: 179.3462 Evaluate side-chains 293 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 798 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 88 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 217 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 225 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 633 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.161618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128826 restraints weight = 82818.366| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.43 r_work: 0.3521 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21383 Z= 0.207 Angle : 0.556 7.106 29065 Z= 0.297 Chirality : 0.040 0.155 3271 Planarity : 0.004 0.047 3754 Dihedral : 4.736 32.327 2923 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.46 % Allowed : 18.76 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2590 helix: 1.21 (0.15), residues: 1287 sheet: -1.98 (0.29), residues: 286 loop : -1.53 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 517 TYR 0.022 0.002 TYR B 497 PHE 0.013 0.002 PHE D 135 TRP 0.015 0.001 TRP B 687 HIS 0.011 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00485 (21383) covalent geometry : angle 0.55593 (29065) hydrogen bonds : bond 0.03888 ( 1025) hydrogen bonds : angle 4.67436 ( 2874) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 560 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue TYR 823 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue VAL 262 is missing expected H atoms. Skipping. Residue TYR 288 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue THR 392 is missing expected H atoms. Skipping. Residue TYR 715 is missing expected H atoms. Skipping. Residue THR 747 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue TYR 753 is missing expected H atoms. Skipping. Residue LEU 754 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 242 time to evaluate : 1.261 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 369 ASN cc_start: 0.5183 (t0) cc_final: 0.4902 (t0) REVERT: B 392 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8645 (p) REVERT: C 378 ASN cc_start: 0.7558 (m110) cc_final: 0.7055 (t0) REVERT: C 723 MET cc_start: 0.5414 (ttm) cc_final: 0.4873 (ptt) REVERT: A 124 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: A 507 ARG cc_start: 0.6131 (mtm180) cc_final: 0.5902 (mtp180) REVERT: A 570 LYS cc_start: 0.5253 (mttm) cc_final: 0.4865 (mptt) REVERT: A 577 GLN cc_start: 0.7196 (mp10) cc_final: 0.6867 (mp10) REVERT: A 609 ASN cc_start: 0.7551 (m110) cc_final: 0.6380 (t0) REVERT: D 433 TYR cc_start: 0.8355 (m-10) cc_final: 0.8104 (m-10) REVERT: D 723 MET cc_start: 0.4821 (tpt) cc_final: 0.4588 (tpt) outliers start: 54 outliers final: 48 residues processed: 284 average time/residue: 0.4203 time to fit residues: 175.4205 Evaluate side-chains 290 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 798 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 23 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 206 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN D 196 HIS ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.163662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131376 restraints weight = 81352.844| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.41 r_work: 0.3556 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21383 Z= 0.121 Angle : 0.502 6.772 29065 Z= 0.265 Chirality : 0.038 0.156 3271 Planarity : 0.004 0.050 3754 Dihedral : 4.518 30.989 2923 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.91 % Allowed : 19.26 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2590 helix: 1.50 (0.15), residues: 1286 sheet: -1.98 (0.29), residues: 288 loop : -1.31 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 517 TYR 0.019 0.001 TYR B 497 PHE 0.008 0.001 PHE A 812 TRP 0.015 0.001 TRP B 687 HIS 0.010 0.001 HIS D 633 Details of bonding type rmsd covalent geometry : bond 0.00280 (21383) covalent geometry : angle 0.50179 (29065) hydrogen bonds : bond 0.03419 ( 1025) hydrogen bonds : angle 4.50221 ( 2874) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 560 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue TYR 823 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue VAL 262 is missing expected H atoms. Skipping. Residue TYR 288 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue THR 392 is missing expected H atoms. Skipping. Residue TYR 715 is missing expected H atoms. Skipping. Residue THR 747 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue TYR 753 is missing expected H atoms. Skipping. Residue LEU 754 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 0.926 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 369 ASN cc_start: 0.5132 (t0) cc_final: 0.4796 (t0) REVERT: B 392 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8664 (p) REVERT: C 378 ASN cc_start: 0.7535 (m110) cc_final: 0.7057 (t0) REVERT: C 392 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8736 (p) REVERT: C 723 MET cc_start: 0.5357 (ttm) cc_final: 0.4870 (ptt) REVERT: A 124 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: A 577 GLN cc_start: 0.7132 (mp10) cc_final: 0.6874 (mp10) REVERT: A 609 ASN cc_start: 0.7542 (m110) cc_final: 0.6394 (t0) REVERT: D 152 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7098 (tp) REVERT: D 433 TYR cc_start: 0.8326 (m-10) cc_final: 0.8090 (m-10) REVERT: D 723 MET cc_start: 0.4839 (tpt) cc_final: 0.4583 (tpt) outliers start: 42 outliers final: 37 residues processed: 283 average time/residue: 0.3808 time to fit residues: 159.2472 Evaluate side-chains 282 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 196 HIS Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 798 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 145 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.163453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131292 restraints weight = 82003.785| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.41 r_work: 0.3554 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 21383 Z= 0.192 Angle : 0.673 57.294 29065 Z= 0.422 Chirality : 0.038 0.155 3271 Planarity : 0.005 0.184 3754 Dihedral : 4.519 31.046 2923 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.96 % Allowed : 19.26 % Favored : 78.78 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2590 helix: 1.50 (0.15), residues: 1286 sheet: -1.98 (0.29), residues: 288 loop : -1.31 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 83 TYR 0.015 0.001 TYR A 635 PHE 0.010 0.001 PHE A 812 TRP 0.015 0.001 TRP B 687 HIS 0.232 0.003 HIS D 196 Details of bonding type rmsd covalent geometry : bond 0.00372 (21383) covalent geometry : angle 0.67291 (29065) hydrogen bonds : bond 0.03455 ( 1025) hydrogen bonds : angle 4.50498 ( 2874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10634.12 seconds wall clock time: 181 minutes 10.08 seconds (10870.08 seconds total)