Starting phenix.real_space_refine (version: dev) on Sun May 15 20:53:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/05_2022/6o6r_0636_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/05_2022/6o6r_0636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/05_2022/6o6r_0636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/05_2022/6o6r_0636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/05_2022/6o6r_0636_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/05_2022/6o6r_0636_updated.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 110": "NH1" <-> "NH2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B ARG 775": "NH1" <-> "NH2" Residue "B ARG 875": "NH1" <-> "NH2" Residue "B ARG 880": "NH1" <-> "NH2" Residue "B GLU 883": "OE1" <-> "OE2" Residue "B GLU 896": "OE1" <-> "OE2" Residue "B GLU 1051": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C GLU 436": "OE1" <-> "OE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C GLU 604": "OE1" <-> "OE2" Residue "C GLU 606": "OE1" <-> "OE2" Residue "C ARG 655": "NH1" <-> "NH2" Residue "C GLU 676": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C GLU 754": "OE1" <-> "OE2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "C ARG 875": "NH1" <-> "NH2" Residue "C ARG 880": "NH1" <-> "NH2" Residue "C GLU 883": "OE1" <-> "OE2" Residue "C GLU 896": "OE1" <-> "OE2" Residue "C GLU 1051": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D GLU 388": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "D GLU 445": "OE1" <-> "OE2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D GLU 604": "OE1" <-> "OE2" Residue "D GLU 606": "OE1" <-> "OE2" Residue "D ARG 655": "NH1" <-> "NH2" Residue "D GLU 676": "OE1" <-> "OE2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D GLU 754": "OE1" <-> "OE2" Residue "D ARG 775": "NH1" <-> "NH2" Residue "D ARG 875": "NH1" <-> "NH2" Residue "D ARG 880": "NH1" <-> "NH2" Residue "D GLU 883": "OE1" <-> "OE2" Residue "D GLU 896": "OE1" <-> "OE2" Residue "D GLU 1051": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 27744 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6812 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 20, 'TRANS': 812} Chain breaks: 9 Chain: "B" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6812 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 20, 'TRANS': 812} Chain breaks: 9 Chain: "C" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6812 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 20, 'TRANS': 812} Chain breaks: 9 Chain: "D" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6812 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 20, 'TRANS': 812} Chain breaks: 9 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 124 Unusual residues: {'LQ7': 1, ' NA': 2, 'Y01': 1, 'UND': 2, '9PE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 124 Unusual residues: {'LQ7': 1, ' NA': 2, 'Y01': 1, 'UND': 2, '9PE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 124 Unusual residues: {'LQ7': 1, ' NA': 2, 'Y01': 1, 'UND': 2, '9PE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 124 Unusual residues: {'LQ7': 1, ' NA': 2, 'Y01': 1, 'UND': 2, '9PE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 17.45, per 1000 atoms: 0.63 Number of scatterers: 27744 At special positions: 0 Unit cell: (128.139, 128.139, 149.319, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 4 15.00 Na 8 11.00 O 4864 8.00 N 4484 7.00 C 18248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.40 Conformation dependent library (CDL) restraints added in 3.9 seconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 173 helices and 4 sheets defined 56.3% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.758A pdb=" N THR A 125 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.546A pdb=" N SER A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.761A pdb=" N TYR A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 removed outlier: 3.595A pdb=" N ILE A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 344 through 347 No H-bonds generated for 'chain 'A' and resid 344 through 347' Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.647A pdb=" N GLU A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 375 " --> pdb=" O TRP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.678A pdb=" N PHE A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 430 through 436 removed outlier: 4.260A pdb=" N ASP A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 462 through 470 Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 494 through 506 Processing helix chain 'A' and resid 510 through 520 removed outlier: 3.502A pdb=" N PHE A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.852A pdb=" N ILE A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.939A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 592 removed outlier: 3.522A pdb=" N LYS A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 625 removed outlier: 3.699A pdb=" N GLU A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 635 Processing helix chain 'A' and resid 649 through 652 No H-bonds generated for 'chain 'A' and resid 649 through 652' Processing helix chain 'A' and resid 657 through 660 No H-bonds generated for 'chain 'A' and resid 657 through 660' Processing helix chain 'A' and resid 663 through 674 Processing helix chain 'A' and resid 684 through 691 removed outlier: 3.726A pdb=" N CYS A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 718 through 721 No H-bonds generated for 'chain 'A' and resid 718 through 721' Processing helix chain 'A' and resid 725 through 748 removed outlier: 3.612A pdb=" N TYR A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 775 removed outlier: 3.757A pdb=" N ILE A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 805 removed outlier: 3.565A pdb=" N ILE A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 802 " --> pdb=" O PHE A 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY A 803 " --> pdb=" O TYR A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 841 removed outlier: 3.552A pdb=" N TYR A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 822 " --> pdb=" O GLY A 818 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 849 removed outlier: 4.042A pdb=" N ILE A 848 " --> pdb=" O PRO A 845 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 849 " --> pdb=" O LYS A 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 845 through 849' Processing helix chain 'A' and resid 854 through 878 removed outlier: 3.564A pdb=" N PHE A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 899 removed outlier: 4.959A pdb=" N ILE A 894 " --> pdb=" O PHE A 890 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR A 895 " --> pdb=" O ARG A 891 " (cutoff:3.500A) Proline residue: A 897 - end of helix Processing helix chain 'A' and resid 945 through 953 Processing helix chain 'A' and resid 956 through 971 removed outlier: 3.666A pdb=" N ASN A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TYR A 971 " --> pdb=" O ALA A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 996 Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1043 through 1058 removed outlier: 3.675A pdb=" N VAL A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A1056 " --> pdb=" O ASN A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1074 No H-bonds generated for 'chain 'A' and resid 1071 through 1074' Processing helix chain 'A' and resid 1076 through 1092 removed outlier: 3.881A pdb=" N LEU A1085 " --> pdb=" O ASP A1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A1089 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.759A pdb=" N THR B 125 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.546A pdb=" N SER B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 268 through 276 removed outlier: 3.761A pdb=" N TYR B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 removed outlier: 3.596A pdb=" N ILE B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 344 through 347 No H-bonds generated for 'chain 'B' and resid 344 through 347' Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 362 through 375 removed outlier: 3.647A pdb=" N GLU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 375 " --> pdb=" O TRP B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 396 through 410 removed outlier: 3.679A pdb=" N PHE B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 Processing helix chain 'B' and resid 430 through 436 removed outlier: 4.261A pdb=" N ASP B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 458 Processing helix chain 'B' and resid 462 through 470 Processing helix chain 'B' and resid 475 through 478 No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 494 through 506 Processing helix chain 'B' and resid 510 through 520 removed outlier: 3.502A pdb=" N PHE B 514 " --> pdb=" O ALA B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 561 removed outlier: 3.852A pdb=" N ILE B 557 " --> pdb=" O GLN B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 574 removed outlier: 3.938A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 592 removed outlier: 3.521A pdb=" N LYS B 590 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 625 removed outlier: 3.698A pdb=" N GLU B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 649 through 652 No H-bonds generated for 'chain 'B' and resid 649 through 652' Processing helix chain 'B' and resid 657 through 660 No H-bonds generated for 'chain 'B' and resid 657 through 660' Processing helix chain 'B' and resid 663 through 674 Processing helix chain 'B' and resid 684 through 691 removed outlier: 3.726A pdb=" N CYS B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 690 " --> pdb=" O ILE B 686 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 691 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 695 No H-bonds generated for 'chain 'B' and resid 693 through 695' Processing helix chain 'B' and resid 718 through 721 No H-bonds generated for 'chain 'B' and resid 718 through 721' Processing helix chain 'B' and resid 725 through 748 removed outlier: 3.613A pdb=" N TYR B 745 " --> pdb=" O LEU B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 775 removed outlier: 3.757A pdb=" N ILE B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 805 removed outlier: 3.565A pdb=" N ILE B 797 " --> pdb=" O ASP B 793 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 802 " --> pdb=" O PHE B 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 803 " --> pdb=" O TYR B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 841 removed outlier: 3.553A pdb=" N TYR B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 821 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 822 " --> pdb=" O GLY B 818 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP B 825 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 849 removed outlier: 4.042A pdb=" N ILE B 848 " --> pdb=" O PRO B 845 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 849 " --> pdb=" O LYS B 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 845 through 849' Processing helix chain 'B' and resid 854 through 878 removed outlier: 3.563A pdb=" N PHE B 859 " --> pdb=" O ILE B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 899 removed outlier: 4.959A pdb=" N ILE B 894 " --> pdb=" O PHE B 890 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR B 895 " --> pdb=" O ARG B 891 " (cutoff:3.500A) Proline residue: B 897 - end of helix Processing helix chain 'B' and resid 945 through 953 Processing helix chain 'B' and resid 956 through 971 removed outlier: 3.666A pdb=" N ASN B 963 " --> pdb=" O ILE B 959 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR B 971 " --> pdb=" O ALA B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 996 Processing helix chain 'B' and resid 1003 through 1005 No H-bonds generated for 'chain 'B' and resid 1003 through 1005' Processing helix chain 'B' and resid 1043 through 1058 removed outlier: 3.675A pdb=" N VAL B1048 " --> pdb=" O ALA B1044 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B1056 " --> pdb=" O ASN B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1071 through 1074 No H-bonds generated for 'chain 'B' and resid 1071 through 1074' Processing helix chain 'B' and resid 1076 through 1092 removed outlier: 3.881A pdb=" N LEU B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B1089 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B1090 " --> pdb=" O LEU B1086 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B1091 " --> pdb=" O LYS B1087 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 removed outlier: 3.758A pdb=" N THR C 125 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 166 removed outlier: 3.546A pdb=" N SER C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 268 through 276 removed outlier: 3.760A pdb=" N TYR C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 311 removed outlier: 3.595A pdb=" N ILE C 307 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 344 through 347 No H-bonds generated for 'chain 'C' and resid 344 through 347' Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 362 through 375 removed outlier: 3.647A pdb=" N GLU C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 375 " --> pdb=" O TRP C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 381 No H-bonds generated for 'chain 'C' and resid 379 through 381' Processing helix chain 'C' and resid 396 through 410 removed outlier: 3.678A pdb=" N PHE C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 426 Processing helix chain 'C' and resid 430 through 436 removed outlier: 4.261A pdb=" N ASP C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 Processing helix chain 'C' and resid 462 through 470 Processing helix chain 'C' and resid 475 through 478 No H-bonds generated for 'chain 'C' and resid 475 through 478' Processing helix chain 'C' and resid 494 through 506 Processing helix chain 'C' and resid 510 through 520 removed outlier: 3.502A pdb=" N PHE C 514 " --> pdb=" O ALA C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 561 removed outlier: 3.851A pdb=" N ILE C 557 " --> pdb=" O GLN C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 574 removed outlier: 3.938A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 592 removed outlier: 3.521A pdb=" N LYS C 590 " --> pdb=" O SER C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 625 removed outlier: 3.700A pdb=" N GLU C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 635 Processing helix chain 'C' and resid 649 through 652 No H-bonds generated for 'chain 'C' and resid 649 through 652' Processing helix chain 'C' and resid 657 through 660 No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 663 through 674 Processing helix chain 'C' and resid 684 through 691 removed outlier: 3.726A pdb=" N CYS C 689 " --> pdb=" O LYS C 685 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 690 " --> pdb=" O ILE C 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 691 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 695 No H-bonds generated for 'chain 'C' and resid 693 through 695' Processing helix chain 'C' and resid 718 through 721 No H-bonds generated for 'chain 'C' and resid 718 through 721' Processing helix chain 'C' and resid 725 through 748 removed outlier: 3.612A pdb=" N TYR C 745 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 775 removed outlier: 3.757A pdb=" N ILE C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 805 removed outlier: 3.565A pdb=" N ILE C 797 " --> pdb=" O ASP C 793 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 802 " --> pdb=" O PHE C 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY C 803 " --> pdb=" O TYR C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 815 No H-bonds generated for 'chain 'C' and resid 812 through 815' Processing helix chain 'C' and resid 820 through 841 removed outlier: 3.542A pdb=" N ASP C 825 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 849 removed outlier: 4.042A pdb=" N ILE C 848 " --> pdb=" O PRO C 845 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C 849 " --> pdb=" O LYS C 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 845 through 849' Processing helix chain 'C' and resid 854 through 878 removed outlier: 3.563A pdb=" N PHE C 859 " --> pdb=" O ILE C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 899 removed outlier: 4.959A pdb=" N ILE C 894 " --> pdb=" O PHE C 890 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR C 895 " --> pdb=" O ARG C 891 " (cutoff:3.500A) Proline residue: C 897 - end of helix Processing helix chain 'C' and resid 945 through 953 Processing helix chain 'C' and resid 956 through 971 removed outlier: 3.666A pdb=" N ASN C 963 " --> pdb=" O ILE C 959 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TYR C 971 " --> pdb=" O ALA C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 996 Processing helix chain 'C' and resid 1003 through 1005 No H-bonds generated for 'chain 'C' and resid 1003 through 1005' Processing helix chain 'C' and resid 1043 through 1058 removed outlier: 3.675A pdb=" N VAL C1048 " --> pdb=" O ALA C1044 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS C1056 " --> pdb=" O ASN C1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 1071 through 1074 No H-bonds generated for 'chain 'C' and resid 1071 through 1074' Processing helix chain 'C' and resid 1076 through 1092 removed outlier: 3.881A pdb=" N LEU C1085 " --> pdb=" O ASP C1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C1089 " --> pdb=" O LEU C1085 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER C1090 " --> pdb=" O LEU C1086 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C1091 " --> pdb=" O LYS C1087 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 125 removed outlier: 3.759A pdb=" N THR D 125 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.545A pdb=" N SER D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 192 Processing helix chain 'D' and resid 268 through 276 removed outlier: 3.760A pdb=" N TYR D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 311 removed outlier: 3.595A pdb=" N ILE D 307 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 344 through 347 No H-bonds generated for 'chain 'D' and resid 344 through 347' Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 362 through 375 removed outlier: 3.647A pdb=" N GLU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 375 " --> pdb=" O TRP D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 396 through 410 removed outlier: 3.677A pdb=" N PHE D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'D' and resid 430 through 436 removed outlier: 4.260A pdb=" N ASP D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 458 Processing helix chain 'D' and resid 462 through 470 Processing helix chain 'D' and resid 475 through 478 No H-bonds generated for 'chain 'D' and resid 475 through 478' Processing helix chain 'D' and resid 494 through 506 Processing helix chain 'D' and resid 510 through 520 removed outlier: 3.502A pdb=" N PHE D 514 " --> pdb=" O ALA D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 561 removed outlier: 3.852A pdb=" N ILE D 557 " --> pdb=" O GLN D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 574 removed outlier: 3.939A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 592 removed outlier: 3.521A pdb=" N LYS D 590 " --> pdb=" O SER D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 625 removed outlier: 3.700A pdb=" N GLU D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 614 " --> pdb=" O ASN D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 635 Processing helix chain 'D' and resid 649 through 652 No H-bonds generated for 'chain 'D' and resid 649 through 652' Processing helix chain 'D' and resid 657 through 660 No H-bonds generated for 'chain 'D' and resid 657 through 660' Processing helix chain 'D' and resid 663 through 674 Processing helix chain 'D' and resid 684 through 691 removed outlier: 3.725A pdb=" N CYS D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 690 " --> pdb=" O ILE D 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 691 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 695 No H-bonds generated for 'chain 'D' and resid 693 through 695' Processing helix chain 'D' and resid 718 through 721 No H-bonds generated for 'chain 'D' and resid 718 through 721' Processing helix chain 'D' and resid 725 through 748 removed outlier: 3.613A pdb=" N TYR D 745 " --> pdb=" O LEU D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 775 removed outlier: 3.758A pdb=" N ILE D 761 " --> pdb=" O ALA D 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU D 773 " --> pdb=" O LEU D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 805 removed outlier: 3.565A pdb=" N ILE D 797 " --> pdb=" O ASP D 793 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 802 " --> pdb=" O PHE D 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY D 803 " --> pdb=" O TYR D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 841 removed outlier: 3.553A pdb=" N TYR D 816 " --> pdb=" O GLU D 812 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER D 817 " --> pdb=" O SER D 813 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 821 " --> pdb=" O SER D 817 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE D 822 " --> pdb=" O GLY D 818 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP D 825 " --> pdb=" O ILE D 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 849 removed outlier: 4.042A pdb=" N ILE D 848 " --> pdb=" O PRO D 845 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET D 849 " --> pdb=" O LYS D 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 845 through 849' Processing helix chain 'D' and resid 854 through 878 removed outlier: 3.564A pdb=" N PHE D 859 " --> pdb=" O ILE D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 899 removed outlier: 4.959A pdb=" N ILE D 894 " --> pdb=" O PHE D 890 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR D 895 " --> pdb=" O ARG D 891 " (cutoff:3.500A) Proline residue: D 897 - end of helix Processing helix chain 'D' and resid 945 through 953 Processing helix chain 'D' and resid 956 through 971 removed outlier: 3.667A pdb=" N ASN D 963 " --> pdb=" O ILE D 959 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TYR D 971 " --> pdb=" O ALA D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 981 through 996 Processing helix chain 'D' and resid 1003 through 1005 No H-bonds generated for 'chain 'D' and resid 1003 through 1005' Processing helix chain 'D' and resid 1043 through 1058 removed outlier: 3.676A pdb=" N VAL D1048 " --> pdb=" O ALA D1044 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D1056 " --> pdb=" O ASN D1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 1071 through 1074 No H-bonds generated for 'chain 'D' and resid 1071 through 1074' Processing helix chain 'D' and resid 1076 through 1092 removed outlier: 3.882A pdb=" N LEU D1085 " --> pdb=" O ASP D1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D1089 " --> pdb=" O LEU D1085 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D1091 " --> pdb=" O LYS D1087 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 168 through 171 removed outlier: 7.137A pdb=" N ASN A 134 " --> pdb=" O TRP A 169 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N PHE A 171 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 136 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 139 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS A 317 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ALA A 296 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 319 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 168 through 171 removed outlier: 7.137A pdb=" N ASN B 134 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N PHE B 171 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 136 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 139 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS B 317 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ALA B 296 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 319 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 168 through 171 removed outlier: 7.137A pdb=" N ASN C 134 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N PHE C 171 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C 136 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C 139 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS C 317 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ALA C 296 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 319 " --> pdb=" O ALA C 296 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 168 through 171 removed outlier: 7.138A pdb=" N ASN D 134 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N PHE D 171 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL D 136 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL D 139 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N CYS D 317 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ALA D 296 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL D 319 " --> pdb=" O ALA D 296 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 3096 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: 10.32 Time building geometry restraints manager: 13.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4332 1.31 - 1.43: 7953 1.43 - 1.56: 15822 1.56 - 1.69: 49 1.69 - 1.82: 220 Bond restraints: 28376 Sorted by residual: bond pdb=" CAI Y01 B1301 " pdb=" CAZ Y01 B1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.25e+02 bond pdb=" CAI Y01 A1301 " pdb=" CAZ Y01 A1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" CAI Y01 C1301 " pdb=" CAZ Y01 C1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" CAI Y01 D1301 " pdb=" CAZ Y01 D1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.23e+02 bond pdb=" CBF Y01 D1301 " pdb=" CBH Y01 D1301 " ideal model delta sigma weight residual 1.550 1.716 -0.166 2.00e-02 2.50e+03 6.86e+01 ... (remaining 28371 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.52: 388 105.52 - 112.72: 14741 112.72 - 119.93: 10805 119.93 - 127.13: 12025 127.13 - 134.34: 365 Bond angle restraints: 38324 Sorted by residual: angle pdb=" C THR C 681 " pdb=" N LYS C 682 " pdb=" CA LYS C 682 " ideal model delta sigma weight residual 121.54 132.49 -10.95 1.91e+00 2.74e-01 3.28e+01 angle pdb=" C THR A 681 " pdb=" N LYS A 682 " pdb=" CA LYS A 682 " ideal model delta sigma weight residual 121.54 132.43 -10.89 1.91e+00 2.74e-01 3.25e+01 angle pdb=" C THR D 681 " pdb=" N LYS D 682 " pdb=" CA LYS D 682 " ideal model delta sigma weight residual 121.54 132.41 -10.87 1.91e+00 2.74e-01 3.24e+01 angle pdb=" C THR B 681 " pdb=" N LYS B 682 " pdb=" CA LYS B 682 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" N PHE B1003 " pdb=" CA PHE B1003 " pdb=" C PHE B1003 " ideal model delta sigma weight residual 113.16 120.14 -6.98 1.42e+00 4.96e-01 2.42e+01 ... (remaining 38319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.34: 15486 24.34 - 48.68: 1038 48.68 - 73.02: 96 73.02 - 97.36: 20 97.36 - 121.70: 4 Dihedral angle restraints: 16644 sinusoidal: 6876 harmonic: 9768 Sorted by residual: dihedral pdb=" CA ILE B 315 " pdb=" C ILE B 315 " pdb=" N PRO B 316 " pdb=" CA PRO B 316 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ILE D 315 " pdb=" C ILE D 315 " pdb=" N PRO D 316 " pdb=" CA PRO D 316 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ILE A 315 " pdb=" C ILE A 315 " pdb=" N PRO A 316 " pdb=" CA PRO A 316 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 16641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4001 0.096 - 0.191: 239 0.191 - 0.287: 18 0.287 - 0.382: 6 0.382 - 0.478: 4 Chirality restraints: 4268 Sorted by residual: chirality pdb=" CBI Y01 C1301 " pdb=" CAU Y01 C1301 " pdb=" CBE Y01 C1301 " pdb=" CBG Y01 C1301 " both_signs ideal model delta sigma weight residual False 2.94 2.46 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CBI Y01 A1301 " pdb=" CAU Y01 A1301 " pdb=" CBE Y01 A1301 " pdb=" CBG Y01 A1301 " both_signs ideal model delta sigma weight residual False 2.94 2.46 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CBI Y01 D1301 " pdb=" CAU Y01 D1301 " pdb=" CBE Y01 D1301 " pdb=" CBG Y01 D1301 " both_signs ideal model delta sigma weight residual False 2.94 2.46 0.48 2.00e-01 2.50e+01 5.66e+00 ... (remaining 4265 not shown) Planarity restraints: 4684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 132 " -0.047 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO D 133 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 133 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 133 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 132 " -0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO A 133 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 132 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO B 133 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " 0.040 5.00e-02 4.00e+02 ... (remaining 4681 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 448 2.67 - 3.23: 25726 3.23 - 3.79: 43322 3.79 - 4.34: 61214 4.34 - 4.90: 95945 Nonbonded interactions: 226655 Sorted by model distance: nonbonded pdb=" CG2 VAL C 768 " pdb=" CZ PHE C1003 " model vdw 2.114 3.760 nonbonded pdb=" CG2 VAL A 768 " pdb=" CZ PHE A1003 " model vdw 2.115 3.760 nonbonded pdb=" CG2 VAL B 768 " pdb=" CZ PHE B1003 " model vdw 2.115 3.760 nonbonded pdb=" CG2 VAL D 768 " pdb=" CZ PHE D1003 " model vdw 2.115 3.760 nonbonded pdb=" CD1 LEU D 769 " pdb=" CZ PHE D1003 " model vdw 2.177 3.760 ... (remaining 226650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 136 5.16 5 Na 8 4.78 5 C 18248 2.51 5 N 4484 2.21 5 O 4864 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.940 Check model and map are aligned: 0.460 Convert atoms to be neutral: 0.250 Process input model: 74.560 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.010 0.360 28376 Z= 0.613 Angle : 1.006 12.498 38324 Z= 0.502 Chirality : 0.057 0.478 4268 Planarity : 0.007 0.072 4684 Dihedral : 15.853 121.697 10292 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.54 (0.09), residues: 3252 helix: -4.46 (0.04), residues: 2176 sheet: -2.72 (0.36), residues: 180 loop : -3.55 (0.16), residues: 896 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 710 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 710 average time/residue: 0.4230 time to fit residues: 466.0936 Evaluate side-chains 526 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 3.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 280 optimal weight: 1.9990 chunk 251 optimal weight: 0.0030 chunk 139 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 260 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 301 optimal weight: 0.0270 overall best weight: 0.4450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS A 248 HIS A 271 GLN A 418 ASN A 471 ASN A 550 HIS A 574 GLN A 597 ASN A1058 ASN B 248 HIS B 418 ASN B 474 ASN B 550 HIS B 553 GLN B 574 GLN B 597 ASN B1058 ASN C 126 GLN C 248 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN C 474 ASN C 553 GLN C 574 GLN C 597 ASN C 610 ASN C1058 ASN D 248 HIS D 271 GLN D 418 ASN D 471 ASN D 550 HIS D 574 GLN D 597 ASN D 610 ASN D 835 HIS D 958 ASN D1058 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 28376 Z= 0.171 Angle : 0.604 11.528 38324 Z= 0.314 Chirality : 0.041 0.173 4268 Planarity : 0.005 0.076 4684 Dihedral : 9.453 88.370 3820 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.11), residues: 3252 helix: -2.44 (0.09), residues: 2176 sheet: -3.01 (0.40), residues: 148 loop : -3.43 (0.16), residues: 928 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 599 time to evaluate : 3.338 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 outliers start: 39 outliers final: 17 residues processed: 619 average time/residue: 0.3963 time to fit residues: 387.5362 Evaluate side-chains 536 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 519 time to evaluate : 3.624 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2635 time to fit residues: 13.0203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 167 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 302 optimal weight: 0.5980 chunk 326 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 299 optimal weight: 0.9980 chunk 102 optimal weight: 0.0010 chunk 242 optimal weight: 4.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 553 GLN C 835 HIS ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 ASN D 553 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 28376 Z= 0.309 Angle : 0.666 14.559 38324 Z= 0.341 Chirality : 0.043 0.164 4268 Planarity : 0.005 0.077 4684 Dihedral : 9.031 79.950 3820 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.13), residues: 3252 helix: -1.40 (0.10), residues: 2176 sheet: -3.22 (0.39), residues: 148 loop : -3.33 (0.17), residues: 928 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 551 time to evaluate : 3.196 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 outliers start: 60 outliers final: 26 residues processed: 589 average time/residue: 0.3923 time to fit residues: 367.5645 Evaluate side-chains 533 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 507 time to evaluate : 3.128 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2389 time to fit residues: 16.0737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 298 optimal weight: 0.0980 chunk 227 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 303 optimal weight: 0.6980 chunk 320 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 287 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN A 776 GLN A 790 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN C 553 GLN C 776 GLN C 790 ASN D 126 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 28376 Z= 0.172 Angle : 0.591 14.837 38324 Z= 0.304 Chirality : 0.041 0.157 4268 Planarity : 0.004 0.086 4684 Dihedral : 8.389 66.936 3820 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.14), residues: 3252 helix: -0.75 (0.11), residues: 2176 sheet: -3.25 (0.41), residues: 144 loop : -3.11 (0.17), residues: 932 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 560 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 11 residues processed: 579 average time/residue: 0.4013 time to fit residues: 370.2475 Evaluate side-chains 510 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 499 time to evaluate : 3.216 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3079 time to fit residues: 10.3200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 267 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 221 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 553 GLN D 126 GLN D 553 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.121 28376 Z= 0.189 Angle : 0.597 14.475 38324 Z= 0.310 Chirality : 0.041 0.174 4268 Planarity : 0.004 0.082 4684 Dihedral : 8.009 60.424 3820 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3252 helix: -0.37 (0.11), residues: 2184 sheet: -3.18 (0.42), residues: 144 loop : -3.07 (0.18), residues: 924 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 545 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 564 average time/residue: 0.3960 time to fit residues: 355.1088 Evaluate side-chains 517 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 500 time to evaluate : 3.236 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3034 time to fit residues: 13.4646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 107 optimal weight: 0.9980 chunk 288 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 321 optimal weight: 0.5980 chunk 266 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 553 GLN B 271 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 501 GLN C 553 GLN D 126 GLN D 553 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.255 28376 Z= 0.234 Angle : 0.623 23.971 38324 Z= 0.335 Chirality : 0.041 0.163 4268 Planarity : 0.004 0.080 4684 Dihedral : 7.807 57.657 3820 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.15), residues: 3252 helix: -0.18 (0.11), residues: 2192 sheet: -3.16 (0.42), residues: 144 loop : -2.98 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 528 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 546 average time/residue: 0.3928 time to fit residues: 343.0424 Evaluate side-chains 511 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 497 time to evaluate : 3.479 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2556 time to fit residues: 11.3718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 309 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 319 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 195 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN C 553 GLN D 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.635 28376 Z= 0.323 Angle : 0.773 73.898 38324 Z= 0.382 Chirality : 0.041 0.200 4268 Planarity : 0.005 0.103 4684 Dihedral : 7.808 57.655 3820 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.15), residues: 3252 helix: -0.15 (0.11), residues: 2192 sheet: -3.15 (0.42), residues: 144 loop : -2.97 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 500 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 515 average time/residue: 0.4289 time to fit residues: 358.3653 Evaluate side-chains 503 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 492 time to evaluate : 3.419 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2897 time to fit residues: 10.3090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 203 optimal weight: 0.3980 chunk 218 optimal weight: 0.0030 chunk 158 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.586 28376 Z= 0.384 Angle : 0.837 73.900 38324 Z= 0.392 Chirality : 0.041 0.246 4268 Planarity : 0.005 0.105 4684 Dihedral : 7.809 57.635 3820 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 3252 helix: -0.13 (0.11), residues: 2192 sheet: -3.15 (0.42), residues: 144 loop : -2.99 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 503 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 506 average time/residue: 0.4039 time to fit residues: 324.7842 Evaluate side-chains 494 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 490 time to evaluate : 3.302 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2577 time to fit residues: 6.4917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 291 optimal weight: 0.3980 chunk 306 optimal weight: 0.7980 chunk 279 optimal weight: 0.5980 chunk 298 optimal weight: 0.9990 chunk 179 optimal weight: 0.0670 chunk 129 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 269 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 297 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS D 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.586 28376 Z= 0.384 Angle : 0.837 73.900 38324 Z= 0.392 Chirality : 0.041 0.246 4268 Planarity : 0.005 0.105 4684 Dihedral : 7.809 57.635 3820 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 3252 helix: -0.13 (0.11), residues: 2192 sheet: -3.15 (0.42), residues: 144 loop : -2.99 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 492 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 493 average time/residue: 0.4153 time to fit residues: 325.5711 Evaluate side-chains 491 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 490 time to evaluate : 3.205 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2515 time to fit residues: 4.9303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 195 optimal weight: 0.7980 chunk 315 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 chunk 219 optimal weight: 0.9990 chunk 330 optimal weight: 5.9990 chunk 304 optimal weight: 0.3980 chunk 263 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS D 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.586 28376 Z= 0.384 Angle : 0.837 73.900 38324 Z= 0.392 Chirality : 0.041 0.246 4268 Planarity : 0.005 0.105 4684 Dihedral : 7.809 57.635 3820 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 3252 helix: -0.13 (0.11), residues: 2192 sheet: -3.15 (0.42), residues: 144 loop : -2.99 (0.18), residues: 916 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 3.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.4187 time to fit residues: 332.2518 Evaluate side-chains 490 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 3.288 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 209 optimal weight: 0.9990 chunk 280 optimal weight: 0.0970 chunk 80 optimal weight: 0.0050 chunk 242 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 270 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS D 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.181879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138687 restraints weight = 33449.438| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.50 r_work: 0.3405 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work: 0.3370 rms_B_bonded: 2.35 restraints_weight: 0.1250 r_work: 0.3351 rms_B_bonded: 2.49 restraints_weight: 0.0625 r_work: 0.3330 rms_B_bonded: 2.69 restraints_weight: 0.0312 r_work: 0.3308 rms_B_bonded: 2.94 restraints_weight: 0.0156 r_work: 0.3282 rms_B_bonded: 3.27 restraints_weight: 0.0078 r_work: 0.3254 rms_B_bonded: 3.67 restraints_weight: 0.0039 r_work: 0.3222 rms_B_bonded: 4.17 restraints_weight: 0.0020 r_work: 0.3185 rms_B_bonded: 4.78 restraints_weight: 0.0010 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.586 28376 Z= 0.384 Angle : 0.837 73.900 38324 Z= 0.392 Chirality : 0.041 0.246 4268 Planarity : 0.005 0.105 4684 Dihedral : 7.809 57.635 3820 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 3252 helix: -0.13 (0.11), residues: 2192 sheet: -3.15 (0.42), residues: 144 loop : -2.99 (0.18), residues: 916 =============================================================================== Job complete usr+sys time: 6377.40 seconds wall clock time: 116 minutes 13.80 seconds (6973.80 seconds total)