Starting phenix.real_space_refine (version: dev) on Sun Feb 26 05:33:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6a_0631/02_2023/6o6a_0631.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6a_0631/02_2023/6o6a_0631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6a_0631/02_2023/6o6a_0631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6a_0631/02_2023/6o6a_0631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6a_0631/02_2023/6o6a_0631.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6a_0631/02_2023/6o6a_0631.pdb" } resolution = 3.6 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "A GLU 185": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 389": "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 607": "OE1" <-> "OE2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" 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 994": "OE1" <-> "OE2" Residue "A PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "B GLU 389": "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 607": "OE1" <-> "OE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" 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 994": "OE1" <-> "OE2" Residue "B PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "C GLU 389": "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 607": "OE1" <-> "OE2" Residue "C GLU 622": "OE1" <-> "OE2" Residue "C ARG 655": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" 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 994": "OE1" <-> "OE2" Residue "C PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D GLU 377": "OE1" <-> "OE2" Residue "D GLU 389": "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 607": "OE1" <-> "OE2" Residue "D GLU 622": "OE1" <-> "OE2" Residue "D ARG 655": "NH1" <-> "NH2" Residue "D ARG 679": "NH1" <-> "NH2" 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 994": "OE1" <-> "OE2" Residue "D PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 27220 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6769 Classifications: {'peptide': 828} Link IDs: {'PTRANS': 20, 'TRANS': 807} Chain breaks: 9 Chain: "B" Number of atoms: 6769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6769 Classifications: {'peptide': 828} Link IDs: {'PTRANS': 20, 'TRANS': 807} Chain breaks: 9 Chain: "C" Number of atoms: 6769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6769 Classifications: {'peptide': 828} Link IDs: {'PTRANS': 20, 'TRANS': 807} Chain breaks: 9 Chain: "D" Number of atoms: 6769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6769 Classifications: {'peptide': 828} Link IDs: {'PTRANS': 20, 'TRANS': 807} Chain breaks: 9 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' NA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' NA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' NA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' NA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.06, per 1000 atoms: 0.55 Number of scatterers: 27220 At special positions: 0 Unit cell: (129.198, 129.198, 148.26, 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 128 16.00 Na 4 11.00 O 4804 8.00 N 4436 7.00 C 17848 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=0, symmetry=0 Time building additional restraints: 10.92 Conformation dependent library (CDL) restraints added in 4.1 seconds 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6320 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 4 sheets defined 66.3% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.957A pdb=" N MET A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 167 removed outlier: 3.631A pdb=" N PHE A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.548A pdb=" N VAL A 186 " --> pdb=" O TYR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 279 removed outlier: 3.506A pdb=" N TYR A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 removed outlier: 3.923A pdb=" N LEU A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.238A pdb=" N ILE A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 358' Processing helix chain 'A' and resid 361 through 374 removed outlier: 3.542A pdb=" N SER A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 395 through 409 removed outlier: 4.082A pdb=" N PHE A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 405 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 4.065A pdb=" N GLN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.690A pdb=" N THR A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.520A pdb=" N LEU A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.741A pdb=" N ILE A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 551 through 562 removed outlier: 4.401A pdb=" N ILE A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 removed outlier: 3.740A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 591 removed outlier: 3.571A pdb=" N ALA A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 626 removed outlier: 3.589A pdb=" N GLU A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 619 " --> pdb=" O ARG A 615 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.533A pdb=" N GLN A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 654 removed outlier: 3.522A pdb=" N ALA A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 662 through 674 Processing helix chain 'A' and resid 683 through 691 removed outlier: 4.133A pdb=" N ILE A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.530A pdb=" N ILE A 696 " --> pdb=" O PHE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 Processing helix chain 'A' and resid 724 through 749 removed outlier: 3.670A pdb=" N ILE A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A 736 " --> pdb=" O ASN A 732 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 772 removed outlier: 3.621A pdb=" N ILE A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 772 " --> pdb=" O VAL A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 789 through 808 removed outlier: 3.525A pdb=" N ILE A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 802 " --> pdb=" O PHE A 798 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 803 " --> pdb=" O TYR A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 842 removed outlier: 3.869A pdb=" N ILE A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 removed outlier: 4.020A pdb=" N ILE A 848 " --> pdb=" O PRO A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 877 Processing helix chain 'A' and resid 888 through 896 removed outlier: 3.595A pdb=" N VAL A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE A 894 " --> pdb=" O PHE A 890 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR A 895 " --> pdb=" O ARG A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 969 removed outlier: 4.223A pdb=" N THR A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.776A pdb=" N TRP A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 985 " --> pdb=" O ASP A 981 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 992 " --> pdb=" O ARG A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.504A pdb=" N VAL A1006 " --> pdb=" O PHE A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1060 removed outlier: 3.626A pdb=" N GLU A1046 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET A1049 " --> pdb=" O TRP A1045 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1092 removed outlier: 3.613A pdb=" N LEU A1082 " --> pdb=" O LYS A1078 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A1087 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU A1088 " --> pdb=" O GLY A1084 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE A1089 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.957A pdb=" N MET B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.630A pdb=" N PHE B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.549A pdb=" N VAL B 186 " --> pdb=" O TYR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 removed outlier: 3.506A pdb=" N TYR B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 279 " --> pdb=" O TYR B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.923A pdb=" N LEU B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 353 through 358 removed outlier: 4.237A pdb=" N ILE B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 358' Processing helix chain 'B' and resid 361 through 374 removed outlier: 3.543A pdb=" N SER B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 395 through 409 removed outlier: 4.083A pdb=" N PHE B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS B 405 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 removed outlier: 4.066A pdb=" N GLN B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 449 through 459 removed outlier: 3.691A pdb=" N THR B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 480 through 491 removed outlier: 3.520A pdb=" N LEU B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 507 removed outlier: 3.740A pdb=" N ILE B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 Processing helix chain 'B' and resid 551 through 562 removed outlier: 4.402A pdb=" N ILE B 557 " --> pdb=" O GLN B 553 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 562 " --> pdb=" O TRP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 removed outlier: 3.740A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 591 removed outlier: 3.571A pdb=" N ALA B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 626 removed outlier: 3.589A pdb=" N GLU B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 615 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.533A pdb=" N GLN B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 654 removed outlier: 3.522A pdb=" N ALA B 651 " --> pdb=" O CYS B 647 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 674 Processing helix chain 'B' and resid 683 through 691 removed outlier: 4.133A pdb=" N ILE B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 691 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.530A pdb=" N ILE B 696 " --> pdb=" O PHE B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 724 through 749 removed outlier: 3.671A pdb=" N ILE B 734 " --> pdb=" O SER B 730 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR B 736 " --> pdb=" O ASN B 732 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 742 " --> pdb=" O ALA B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 772 removed outlier: 3.621A pdb=" N ILE B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 762 " --> pdb=" O LEU B 758 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 789 through 808 removed outlier: 3.525A pdb=" N ILE B 797 " --> pdb=" O ASP B 793 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 802 " --> pdb=" O PHE B 798 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B 803 " --> pdb=" O TYR B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 842 removed outlier: 3.870A pdb=" N ILE B 821 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP B 825 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 removed outlier: 4.020A pdb=" N ILE B 848 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 877 Processing helix chain 'B' and resid 888 through 896 removed outlier: 3.595A pdb=" N VAL B 893 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE B 894 " --> pdb=" O PHE B 890 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR B 895 " --> pdb=" O ARG B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 969 removed outlier: 4.223A pdb=" N THR B 957 " --> pdb=" O TYR B 953 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 963 " --> pdb=" O ILE B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 997 removed outlier: 3.777A pdb=" N TRP B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 985 " --> pdb=" O ASP B 981 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 992 " --> pdb=" O ARG B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1006 removed outlier: 3.504A pdb=" N VAL B1006 " --> pdb=" O PHE B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1060 removed outlier: 3.626A pdb=" N GLU B1046 " --> pdb=" O ILE B1042 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B1048 " --> pdb=" O ALA B1044 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET B1049 " --> pdb=" O TRP B1045 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN B1058 " --> pdb=" O LEU B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1092 removed outlier: 3.612A pdb=" N LEU B1082 " --> pdb=" O LYS B1078 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B1083 " --> pdb=" O LEU B1079 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B1087 " --> pdb=" O LYS B1083 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLU B1088 " --> pdb=" O GLY B1084 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE B1089 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B1090 " --> pdb=" O LEU B1086 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B1091 " --> pdb=" O LYS B1087 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.957A pdb=" N MET C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 167 removed outlier: 3.631A pdb=" N PHE C 156 " --> pdb=" O MET C 152 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.548A pdb=" N VAL C 186 " --> pdb=" O TYR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 279 removed outlier: 3.506A pdb=" N TYR C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 279 " --> pdb=" O TYR C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.923A pdb=" N LEU C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 333 Processing helix chain 'C' and resid 353 through 358 removed outlier: 4.237A pdb=" N ILE C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 358' Processing helix chain 'C' and resid 361 through 374 removed outlier: 3.542A pdb=" N SER C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 370 " --> pdb=" O GLU C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 395 through 409 removed outlier: 4.083A pdb=" N PHE C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 405 " --> pdb=" O PHE C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 4.066A pdb=" N GLN C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 Processing helix chain 'C' and resid 449 through 459 removed outlier: 3.690A pdb=" N THR C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 458 " --> pdb=" O PHE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 471 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 480 through 491 removed outlier: 3.519A pdb=" N LEU C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN C 490 " --> pdb=" O GLU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 507 removed outlier: 3.741A pdb=" N ILE C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 Processing helix chain 'C' and resid 551 through 562 removed outlier: 4.401A pdb=" N ILE C 557 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN C 562 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 removed outlier: 3.741A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 591 removed outlier: 3.571A pdb=" N ALA C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU C 583 " --> pdb=" O THR C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 626 removed outlier: 3.589A pdb=" N GLU C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 615 " --> pdb=" O GLU C 611 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 618 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 619 " --> pdb=" O ARG C 615 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 636 removed outlier: 3.532A pdb=" N GLN C 633 " --> pdb=" O ASP C 629 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 654 removed outlier: 3.523A pdb=" N ALA C 651 " --> pdb=" O CYS C 647 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 662 through 674 Processing helix chain 'C' and resid 683 through 691 removed outlier: 4.133A pdb=" N ILE C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS C 689 " --> pdb=" O LYS C 685 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 691 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.530A pdb=" N ILE C 696 " --> pdb=" O PHE C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 722 Processing helix chain 'C' and resid 724 through 749 removed outlier: 3.670A pdb=" N ILE C 734 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR C 736 " --> pdb=" O ASN C 732 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 742 " --> pdb=" O ALA C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 772 removed outlier: 3.622A pdb=" N ILE C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 772 " --> pdb=" O VAL C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 777 Processing helix chain 'C' and resid 789 through 808 removed outlier: 3.525A pdb=" N ILE C 797 " --> pdb=" O ASP C 793 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 802 " --> pdb=" O PHE C 798 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 803 " --> pdb=" O TYR C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 842 removed outlier: 3.869A pdb=" N ILE C 821 " --> pdb=" O SER C 817 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP C 825 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 848 removed outlier: 4.021A pdb=" N ILE C 848 " --> pdb=" O PRO C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 877 Processing helix chain 'C' and resid 888 through 896 removed outlier: 3.594A pdb=" N VAL C 893 " --> pdb=" O ILE C 889 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE C 894 " --> pdb=" O PHE C 890 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR C 895 " --> pdb=" O ARG C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 969 removed outlier: 4.223A pdb=" N THR C 957 " --> pdb=" O TYR C 953 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 963 " --> pdb=" O ILE C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.776A pdb=" N TRP C 984 " --> pdb=" O ASN C 980 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 985 " --> pdb=" O ASP C 981 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 992 " --> pdb=" O ARG C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1006 removed outlier: 3.503A pdb=" N VAL C1006 " --> pdb=" O PHE C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1060 removed outlier: 3.627A pdb=" N GLU C1046 " --> pdb=" O ILE C1042 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL C1048 " --> pdb=" O ALA C1044 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C1049 " --> pdb=" O TRP C1045 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C1058 " --> pdb=" O LEU C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1072 through 1092 removed outlier: 3.612A pdb=" N LEU C1082 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS C1083 " --> pdb=" O LEU C1079 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C1087 " --> pdb=" O LYS C1083 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU C1088 " --> pdb=" O GLY C1084 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE C1089 " --> pdb=" O LEU C1085 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER C1090 " --> pdb=" O LEU C1086 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C1091 " --> pdb=" O LYS C1087 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.957A pdb=" N MET D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 167 removed outlier: 3.630A pdb=" N PHE D 156 " --> pdb=" O MET D 152 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 190 removed outlier: 3.548A pdb=" N VAL D 186 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 279 removed outlier: 3.505A pdb=" N TYR D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 279 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 removed outlier: 3.923A pdb=" N LEU D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 353 through 358 removed outlier: 4.238A pdb=" N ILE D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 353 through 358' Processing helix chain 'D' and resid 361 through 374 removed outlier: 3.542A pdb=" N SER D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE D 369 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 370 " --> pdb=" O GLU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 380 No H-bonds generated for 'chain 'D' and resid 378 through 380' Processing helix chain 'D' and resid 395 through 409 removed outlier: 4.082A pdb=" N PHE D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS D 405 " --> pdb=" O PHE D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 4.065A pdb=" N GLN D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 437 Processing helix chain 'D' and resid 449 through 459 removed outlier: 3.690A pdb=" N THR D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 458 " --> pdb=" O PHE D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 480 through 491 removed outlier: 3.520A pdb=" N LEU D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN D 490 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 507 removed outlier: 3.742A pdb=" N ILE D 502 " --> pdb=" O LYS D 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 507 " --> pdb=" O ALA D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 Processing helix chain 'D' and resid 551 through 562 removed outlier: 4.401A pdb=" N ILE D 557 " --> pdb=" O GLN D 553 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN D 562 " --> pdb=" O TRP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 573 removed outlier: 3.741A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 591 removed outlier: 3.571A pdb=" N ALA D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 626 removed outlier: 3.589A pdb=" N GLU D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 615 " --> pdb=" O GLU D 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 618 " --> pdb=" O THR D 614 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 619 " --> pdb=" O ARG D 615 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.534A pdb=" N GLN D 633 " --> pdb=" O ASP D 629 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 654 removed outlier: 3.522A pdb=" N ALA D 651 " --> pdb=" O CYS D 647 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 662 through 674 Processing helix chain 'D' and resid 683 through 691 removed outlier: 4.134A pdb=" N ILE D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 691 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 696 removed outlier: 3.530A pdb=" N ILE D 696 " --> pdb=" O PHE D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 722 Processing helix chain 'D' and resid 724 through 749 removed outlier: 3.671A pdb=" N ILE D 734 " --> pdb=" O SER D 730 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR D 736 " --> pdb=" O ASN D 732 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 742 " --> pdb=" O ALA D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 772 removed outlier: 3.621A pdb=" N ILE D 761 " --> pdb=" O ALA D 757 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 762 " --> pdb=" O LEU D 758 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 772 " --> pdb=" O VAL D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 777 Processing helix chain 'D' and resid 789 through 808 removed outlier: 3.525A pdb=" N ILE D 797 " --> pdb=" O ASP D 793 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 802 " --> pdb=" O PHE D 798 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 803 " --> pdb=" O TYR D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 842 removed outlier: 3.869A pdb=" N ILE D 821 " --> pdb=" O SER D 817 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP D 825 " --> pdb=" O ILE D 821 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 842 " --> pdb=" O THR D 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 848 removed outlier: 4.020A pdb=" N ILE D 848 " --> pdb=" O PRO D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 877 Processing helix chain 'D' and resid 888 through 896 removed outlier: 3.594A pdb=" N VAL D 893 " --> pdb=" O ILE D 889 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE D 894 " --> pdb=" O PHE D 890 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR D 895 " --> pdb=" O ARG D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 969 removed outlier: 4.223A pdb=" N THR D 957 " --> pdb=" O TYR D 953 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN D 963 " --> pdb=" O ILE D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 997 removed outlier: 3.776A pdb=" N TRP D 984 " --> pdb=" O ASN D 980 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D 985 " --> pdb=" O ASP D 981 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 992 " --> pdb=" O ARG D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1006 removed outlier: 3.503A pdb=" N VAL D1006 " --> pdb=" O PHE D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1060 removed outlier: 3.626A pdb=" N GLU D1046 " --> pdb=" O ILE D1042 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL D1048 " --> pdb=" O ALA D1044 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET D1049 " --> pdb=" O TRP D1045 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN D1058 " --> pdb=" O LEU D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1072 through 1092 removed outlier: 3.613A pdb=" N LEU D1082 " --> pdb=" O LYS D1078 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D1083 " --> pdb=" O LEU D1079 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D1085 " --> pdb=" O ASP D1081 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS D1087 " --> pdb=" O LYS D1083 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU D1088 " --> pdb=" O GLY D1084 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE D1089 " --> pdb=" O LEU D1085 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D1091 " --> pdb=" O LYS D1087 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 250 through 252 removed outlier: 6.514A pdb=" N ALA A 202 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU A 252 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY A 204 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE A 170 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 205 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR A 172 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 135 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE A 295 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE A 137 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 317 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 321 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 318 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 385 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 320 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 250 through 252 removed outlier: 6.514A pdb=" N ALA B 202 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU B 252 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY B 204 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE B 170 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 205 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N THR B 172 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU B 135 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE B 295 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE B 137 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 317 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU B 321 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 318 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE B 385 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 320 " --> pdb=" O ILE B 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 250 through 252 removed outlier: 6.514A pdb=" N ALA C 202 " --> pdb=" O HIS C 250 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU C 252 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY C 204 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE C 170 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE C 205 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR C 172 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 135 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE C 295 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE C 137 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS C 317 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 321 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 318 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE C 385 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 320 " --> pdb=" O ILE C 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 250 through 252 removed outlier: 6.514A pdb=" N ALA D 202 " --> pdb=" O HIS D 250 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU D 252 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY D 204 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE D 170 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE D 205 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR D 172 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU D 135 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE D 295 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE D 137 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS D 317 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU D 321 " --> pdb=" O ALA D 296 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 318 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE D 385 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 320 " --> pdb=" O ILE D 385 " (cutoff:3.500A) 1238 hydrogen bonds defined for protein. 3678 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: 8.80 Time building geometry restraints manager: 11.45 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: 4304 1.31 - 1.44: 7821 1.44 - 1.56: 15483 1.56 - 1.69: 36 1.69 - 1.82: 212 Bond restraints: 27856 Sorted by residual: bond pdb=" CAI Y01 D1301 " pdb=" CAZ Y01 D1301 " ideal model delta sigma weight residual 1.332 1.695 -0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" CAI Y01 B1301 " pdb=" CAZ Y01 B1301 " ideal model delta sigma weight residual 1.332 1.695 -0.363 2.00e-02 2.50e+03 3.29e+02 bond pdb=" CAI Y01 A1301 " pdb=" CAZ Y01 A1301 " ideal model delta sigma weight residual 1.332 1.695 -0.363 2.00e-02 2.50e+03 3.29e+02 bond pdb=" CAI Y01 C1301 " pdb=" CAZ Y01 C1301 " ideal model delta sigma weight residual 1.332 1.695 -0.363 2.00e-02 2.50e+03 3.29e+02 bond pdb=" CBB Y01 C1301 " pdb=" CBE Y01 C1301 " ideal model delta sigma weight residual 1.535 1.376 0.159 2.00e-02 2.50e+03 6.35e+01 ... (remaining 27851 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.78: 607 106.78 - 113.62: 15270 113.62 - 120.47: 11803 120.47 - 127.31: 9700 127.31 - 134.15: 328 Bond angle restraints: 37708 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 121.54 132.97 -11.43 1.91e+00 2.74e-01 3.58e+01 angle pdb=" C THR A 681 " pdb=" N LYS A 682 " pdb=" CA LYS A 682 " ideal model delta sigma weight residual 121.54 132.96 -11.42 1.91e+00 2.74e-01 3.58e+01 angle pdb=" C THR B 681 " pdb=" N LYS B 682 " pdb=" CA LYS B 682 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" C THR D 681 " pdb=" N LYS D 682 " pdb=" CA LYS D 682 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" N PHE B1003 " pdb=" CA PHE B1003 " pdb=" C PHE B1003 " ideal model delta sigma weight residual 113.16 121.63 -8.47 1.42e+00 4.96e-01 3.56e+01 ... (remaining 37703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 14432 17.85 - 35.70: 1533 35.70 - 53.56: 295 53.56 - 71.41: 52 71.41 - 89.26: 32 Dihedral angle restraints: 16344 sinusoidal: 6628 harmonic: 9716 Sorted by residual: 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 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 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 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ILE C 315 " pdb=" C ILE C 315 " pdb=" N PRO C 316 " pdb=" CA PRO C 316 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 16341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3993 0.098 - 0.195: 235 0.195 - 0.293: 8 0.293 - 0.391: 4 0.391 - 0.489: 8 Chirality restraints: 4248 Sorted by residual: chirality pdb=" CBF Y01 A1301 " pdb=" CAS Y01 A1301 " pdb=" CBD Y01 A1301 " pdb=" CBH Y01 A1301 " both_signs ideal model delta sigma weight residual False -2.45 -2.93 0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" CBF Y01 C1301 " pdb=" CAS Y01 C1301 " pdb=" CBD Y01 C1301 " pdb=" CBH Y01 C1301 " both_signs ideal model delta sigma weight residual False -2.45 -2.93 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CBF Y01 B1301 " pdb=" CAS Y01 B1301 " pdb=" CBD Y01 B1301 " pdb=" CBH Y01 B1301 " both_signs ideal model delta sigma weight residual False -2.45 -2.93 0.49 2.00e-01 2.50e+01 5.93e+00 ... (remaining 4245 not shown) Planarity restraints: 4632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 958 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" CG ASN C 958 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN C 958 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 958 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 958 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.05e+00 pdb=" CG ASN A 958 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 958 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 958 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 958 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" CG ASN D 958 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN D 958 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN D 958 " 0.015 2.00e-02 2.50e+03 ... (remaining 4629 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 189 2.57 - 3.15: 20936 3.15 - 3.73: 41751 3.73 - 4.32: 59092 4.32 - 4.90: 93736 Nonbonded interactions: 215704 Sorted by model distance: nonbonded pdb=" O THR B 575 " pdb=" NZ LYS B1050 " model vdw 1.986 2.520 nonbonded pdb=" O THR C 575 " pdb=" NZ LYS C1050 " model vdw 1.986 2.520 nonbonded pdb=" O THR A 575 " pdb=" NZ LYS A1050 " model vdw 1.987 2.520 nonbonded pdb=" O THR D 575 " pdb=" NZ LYS D1050 " model vdw 1.987 2.520 nonbonded pdb=" SG CYS C 578 " pdb=" NZ LYS C1050 " model vdw 2.179 2.880 ... (remaining 215699 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: 5 Type Number sf(0) Gaussians S 128 5.16 5 Na 4 4.78 5 C 17848 2.51 5 N 4436 2.21 5 O 4804 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 8.370 Check model and map are aligned: 0.410 Process input model: 67.330 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.240 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.363 27856 Z= 0.542 Angle : 0.988 16.268 37708 Z= 0.523 Chirality : 0.056 0.489 4248 Planarity : 0.006 0.062 4632 Dihedral : 15.673 89.262 10024 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % 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: -6.33 (0.09), residues: 3232 helix: -4.42 (0.05), residues: 2100 sheet: -3.11 (0.32), residues: 144 loop : -3.19 (0.16), residues: 988 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1039 time to evaluate : 3.421 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 outliers start: 0 outliers final: 0 residues processed: 1039 average time/residue: 0.4240 time to fit residues: 692.9255 Evaluate side-chains 793 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 793 time to evaluate : 3.336 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 167 optimal weight: 0.0870 chunk 132 optimal weight: 0.9980 chunk 257 optimal weight: 0.7980 chunk 99 optimal weight: 0.0370 chunk 156 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 297 optimal weight: 0.0980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN A 550 HIS A 563 ASN A 597 ASN A 662 GLN A 790 ASN ** A 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN A1052 ASN A1074 GLN B 127 HIS B 248 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 550 HIS B 563 ASN B 597 ASN ** B 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN B1052 ASN C 127 HIS C 248 HIS ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 563 ASN C 662 GLN ** C 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1052 ASN D 127 HIS D 248 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 ASN D 491 ASN D 550 HIS D 563 ASN D 662 GLN D 667 ASN D 790 ASN ** D 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 958 ASN D 963 ASN D 979 ASN D 980 ASN D1052 ASN D1070 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 27856 Z= 0.170 Angle : 0.648 11.769 37708 Z= 0.335 Chirality : 0.042 0.232 4248 Planarity : 0.005 0.050 4632 Dihedral : 6.549 56.187 3604 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 2.50 % 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: -4.24 (0.11), residues: 3232 helix: -2.49 (0.08), residues: 2180 sheet: -2.77 (0.35), residues: 144 loop : -3.09 (0.17), residues: 908 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 967 time to evaluate : 3.109 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 outliers start: 74 outliers final: 35 residues processed: 994 average time/residue: 0.3688 time to fit residues: 586.7356 Evaluate side-chains 869 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 834 time to evaluate : 3.236 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2506 time to fit residues: 21.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 0.0970 chunk 92 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 202 optimal weight: 0.1980 chunk 82 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 322 optimal weight: 0.6980 chunk 265 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 GLN ** C1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 429 GLN D 597 ASN D 963 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 27856 Z= 0.201 Angle : 0.626 12.460 37708 Z= 0.317 Chirality : 0.042 0.214 4248 Planarity : 0.004 0.054 4632 Dihedral : 6.107 59.722 3604 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 3.18 % 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: -3.03 (0.13), residues: 3232 helix: -1.46 (0.10), residues: 2176 sheet: -2.67 (0.37), residues: 144 loop : -2.90 (0.18), residues: 912 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 886 time to evaluate : 3.087 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 outliers start: 94 outliers final: 43 residues processed: 926 average time/residue: 0.3679 time to fit residues: 554.2651 Evaluate side-chains 851 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 808 time to evaluate : 3.273 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2568 time to fit residues: 25.7415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 317 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 491 ASN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN D 471 ASN ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 ASN D 876 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 27856 Z= 0.208 Angle : 0.640 12.709 37708 Z= 0.318 Chirality : 0.042 0.206 4248 Planarity : 0.004 0.052 4632 Dihedral : 5.952 58.421 3604 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 2.13 % 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: -2.42 (0.14), residues: 3232 helix: -0.96 (0.11), residues: 2180 sheet: -2.38 (0.39), residues: 144 loop : -2.76 (0.18), residues: 908 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 880 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 35 residues processed: 902 average time/residue: 0.3763 time to fit residues: 545.6519 Evaluate side-chains 862 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 827 time to evaluate : 3.115 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2605 time to fit residues: 21.0510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 236 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 284 optimal weight: 3.9990 chunk 80 optimal weight: 0.0050 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 ASN D 835 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 27856 Z= 0.182 Angle : 0.632 12.771 37708 Z= 0.310 Chirality : 0.042 0.272 4248 Planarity : 0.004 0.053 4632 Dihedral : 5.775 59.035 3604 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer Outliers : 1.42 % 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: -2.07 (0.14), residues: 3232 helix: -0.63 (0.11), residues: 2164 sheet: -2.25 (0.40), residues: 144 loop : -2.78 (0.18), residues: 924 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 892 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 911 average time/residue: 0.3923 time to fit residues: 575.6755 Evaluate side-chains 847 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 828 time to evaluate : 3.266 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2955 time to fit residues: 14.7722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 0.9980 chunk 285 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 317 optimal weight: 0.0470 chunk 263 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 104 optimal weight: 0.0040 chunk 166 optimal weight: 3.9990 overall best weight: 0.5090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 790 ASN C 963 ASN ** C1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 835 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 27856 Z= 0.172 Angle : 0.639 12.937 37708 Z= 0.313 Chirality : 0.042 0.288 4248 Planarity : 0.004 0.052 4632 Dihedral : 5.660 56.894 3604 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % 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: -1.70 (0.14), residues: 3232 helix: -0.39 (0.11), residues: 2160 sheet: -2.07 (0.41), residues: 144 loop : -2.55 (0.18), residues: 928 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 882 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 899 average time/residue: 0.3778 time to fit residues: 541.7944 Evaluate side-chains 856 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 839 time to evaluate : 2.928 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2350 time to fit residues: 11.9022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 316 optimal weight: 0.0670 chunk 197 optimal weight: 4.9990 chunk 192 optimal weight: 0.2980 chunk 145 optimal weight: 2.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 HIS ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN C 429 GLN ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 ASN C 963 ASN ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 835 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 27856 Z= 0.208 Angle : 0.660 13.192 37708 Z= 0.325 Chirality : 0.043 0.255 4248 Planarity : 0.004 0.052 4632 Dihedral : 5.641 56.304 3604 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 1.89 % 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: -1.53 (0.14), residues: 3232 helix: -0.23 (0.11), residues: 2164 sheet: -1.88 (0.43), residues: 144 loop : -2.58 (0.18), residues: 924 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 864 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 34 residues processed: 890 average time/residue: 0.3976 time to fit residues: 572.4754 Evaluate side-chains 864 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 830 time to evaluate : 3.153 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2705 time to fit residues: 21.6639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 95 optimal weight: 0.0570 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 215 optimal weight: 0.4980 chunk 156 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 835 HIS D 958 ASN D1052 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 27856 Z= 0.197 Angle : 0.666 13.095 37708 Z= 0.326 Chirality : 0.043 0.263 4248 Planarity : 0.004 0.052 4632 Dihedral : 5.607 55.439 3604 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.21 (0.15), residues: 3232 helix: 0.01 (0.11), residues: 2128 sheet: -1.72 (0.43), residues: 144 loop : -2.37 (0.19), residues: 960 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 867 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 886 average time/residue: 0.3708 time to fit residues: 528.2573 Evaluate side-chains 842 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 823 time to evaluate : 2.916 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2567 time to fit residues: 13.4110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 0.7980 chunk 302 optimal weight: 0.0870 chunk 276 optimal weight: 0.5980 chunk 294 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 278 optimal weight: 0.6980 chunk 293 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN A 501 GLN A 657 GLN A 776 GLN B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN C 979 ASN D 176 HIS D 428 ASN ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 ASN D 835 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 27856 Z= 0.185 Angle : 0.670 13.882 37708 Z= 0.323 Chirality : 0.042 0.241 4248 Planarity : 0.004 0.052 4632 Dihedral : 5.606 55.046 3604 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.03 % 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: -1.15 (0.14), residues: 3232 helix: 0.05 (0.11), residues: 2172 sheet: -1.59 (0.44), residues: 144 loop : -2.45 (0.19), residues: 916 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 866 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 880 average time/residue: 0.3829 time to fit residues: 542.5696 Evaluate side-chains 838 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 822 time to evaluate : 3.375 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2671 time to fit residues: 12.9589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 0.6980 chunk 311 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 147 optimal weight: 0.0060 chunk 216 optimal weight: 5.9990 chunk 326 optimal weight: 0.2980 chunk 300 optimal weight: 0.0970 chunk 260 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 159 optimal weight: 0.5980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN C 563 ASN C 835 HIS C 963 ASN ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 27856 Z= 0.176 Angle : 0.688 14.708 37708 Z= 0.329 Chirality : 0.042 0.213 4248 Planarity : 0.004 0.053 4632 Dihedral : 5.544 54.630 3604 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3232 helix: 0.18 (0.11), residues: 2156 sheet: -1.45 (0.44), residues: 144 loop : -2.31 (0.19), residues: 932 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 876 time to evaluate : 3.405 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 outliers start: 12 outliers final: 7 residues processed: 883 average time/residue: 0.3738 time to fit residues: 536.0645 Evaluate side-chains 840 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 833 time to evaluate : 3.183 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2489 time to fit residues: 8.0242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 1.9990 chunk 277 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 267 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 GLN C 790 ASN C 963 ASN ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 776 GLN D 882 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.172805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.142378 restraints weight = 42635.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.146564 restraints weight = 24745.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149232 restraints weight = 17807.019| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 27856 Z= 0.255 Angle : 0.715 13.341 37708 Z= 0.348 Chirality : 0.044 0.230 4248 Planarity : 0.004 0.051 4632 Dihedral : 5.694 54.956 3604 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 0.91 % 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: -1.00 (0.15), residues: 3232 helix: 0.14 (0.11), residues: 2140 sheet: -1.43 (0.45), residues: 144 loop : -2.29 (0.19), residues: 948 =============================================================================== Job complete usr+sys time: 8240.55 seconds wall clock time: 149 minutes 4.98 seconds (8944.98 seconds total)