Starting phenix.real_space_refine on Wed Mar 20 11:19:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6a_0631/03_2024/6o6a_0631.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6a_0631/03_2024/6o6a_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_0631/03_2024/6o6a_0631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6a_0631/03_2024/6o6a_0631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6a_0631/03_2024/6o6a_0631.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6a_0631/03_2024/6o6a_0631.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.61, per 1000 atoms: 0.50 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: 9.67 Conformation dependent library (CDL) restraints added in 4.6 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: 2.48 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: 8.53 Time building geometry restraints manager: 10.54 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: 14608 17.85 - 35.70: 1577 35.70 - 53.56: 307 53.56 - 71.41: 52 71.41 - 89.26: 32 Dihedral angle restraints: 16576 sinusoidal: 6860 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 16573 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 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: 1.640 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: 7.040 Check model and map are aligned: 0.430 Set scattering table: 0.220 Process input model: 64.980 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 15.679 89.262 10256 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 984 HIS 0.004 0.001 HIS D 176 PHE 0.033 0.002 PHE C 700 TYR 0.016 0.001 TYR C 121 ARG 0.004 0.000 ARG A 485 *********************** 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 : 2.814 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: A 135 LEU cc_start: 0.9150 (tt) cc_final: 0.8876 (tt) REVERT: A 460 ASP cc_start: 0.7890 (t0) cc_final: 0.7543 (t70) REVERT: A 604 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7819 (mm-30) REVERT: A 655 ARG cc_start: 0.8730 (mtp85) cc_final: 0.8499 (ttm110) REVERT: A 682 LYS cc_start: 0.9312 (mmmm) cc_final: 0.8871 (mmmm) REVERT: A 731 TRP cc_start: 0.8214 (t-100) cc_final: 0.7941 (t-100) REVERT: A 835 HIS cc_start: 0.8540 (t70) cc_final: 0.8339 (t70) REVERT: A 856 ASP cc_start: 0.8473 (m-30) cc_final: 0.8265 (m-30) REVERT: A 868 MET cc_start: 0.8709 (mmm) cc_final: 0.8471 (mmm) REVERT: A 896 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7545 (mt-10) REVERT: A 963 ASN cc_start: 0.8546 (m-40) cc_final: 0.8305 (m-40) REVERT: A 980 ASN cc_start: 0.8233 (t0) cc_final: 0.7883 (m110) REVERT: A 990 PHE cc_start: 0.8353 (t80) cc_final: 0.8081 (t80) REVERT: B 121 TYR cc_start: 0.6660 (t80) cc_final: 0.5983 (t80) REVERT: B 366 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8456 (mm-30) REVERT: B 453 MET cc_start: 0.8958 (tpp) cc_final: 0.8696 (tpp) REVERT: B 463 LYS cc_start: 0.9007 (mttm) cc_final: 0.8477 (mtmm) REVERT: B 626 ASN cc_start: 0.8067 (m-40) cc_final: 0.6997 (m-40) REVERT: B 655 ARG cc_start: 0.8812 (mtp85) cc_final: 0.8512 (ttm110) REVERT: B 736 TYR cc_start: 0.9082 (t80) cc_final: 0.8847 (t80) REVERT: B 867 TRP cc_start: 0.9168 (t60) cc_final: 0.8921 (t60) REVERT: B 980 ASN cc_start: 0.8328 (t0) cc_final: 0.7844 (m110) REVERT: B 985 LYS cc_start: 0.9348 (mttm) cc_final: 0.9078 (mttt) REVERT: B 1070 HIS cc_start: 0.7500 (p-80) cc_final: 0.7156 (p-80) REVERT: B 1071 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7918 (mmm-85) REVERT: C 135 LEU cc_start: 0.9192 (tt) cc_final: 0.8900 (tt) REVERT: C 164 GLN cc_start: 0.8510 (tp40) cc_final: 0.7907 (tp40) REVERT: C 245 ASP cc_start: 0.8731 (t0) cc_final: 0.8280 (t0) REVERT: C 271 GLN cc_start: 0.6410 (tm-30) cc_final: 0.6026 (tm-30) REVERT: C 460 ASP cc_start: 0.8199 (t0) cc_final: 0.7970 (t70) REVERT: C 655 ARG cc_start: 0.8765 (mtp85) cc_final: 0.8563 (ttm110) REVERT: C 736 TYR cc_start: 0.9037 (t80) cc_final: 0.8796 (t80) REVERT: C 775 ARG cc_start: 0.6865 (mmm160) cc_final: 0.6505 (ptp-170) REVERT: C 856 ASP cc_start: 0.8306 (m-30) cc_final: 0.8078 (m-30) REVERT: C 867 TRP cc_start: 0.9140 (t60) cc_final: 0.8867 (t60) REVERT: C 963 ASN cc_start: 0.8424 (m-40) cc_final: 0.8185 (m-40) REVERT: C 980 ASN cc_start: 0.8364 (t0) cc_final: 0.7974 (m110) REVERT: C 985 LYS cc_start: 0.9306 (mttm) cc_final: 0.9037 (mttt) REVERT: C 990 PHE cc_start: 0.8308 (t80) cc_final: 0.7983 (t80) REVERT: C 1051 GLU cc_start: 0.8953 (tp30) cc_final: 0.8641 (tp30) REVERT: C 1068 MET cc_start: 0.5503 (pmm) cc_final: 0.5302 (pmm) REVERT: C 1081 ASP cc_start: 0.8662 (t0) cc_final: 0.8452 (t70) REVERT: D 153 ARG cc_start: 0.8671 (ptp-110) cc_final: 0.8471 (mtm110) REVERT: D 164 GLN cc_start: 0.8351 (tp40) cc_final: 0.7908 (tp40) REVERT: D 271 GLN cc_start: 0.5920 (tm-30) cc_final: 0.5608 (tm-30) REVERT: D 346 LYS cc_start: 0.6317 (mptt) cc_final: 0.5425 (tppt) REVERT: D 365 THR cc_start: 0.5144 (m) cc_final: 0.4744 (m) REVERT: D 366 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8304 (mm-30) REVERT: D 463 LYS cc_start: 0.8990 (mttm) cc_final: 0.8604 (mtmm) REVERT: D 479 LEU cc_start: 0.9231 (mt) cc_final: 0.8925 (mt) REVERT: D 484 LEU cc_start: 0.9353 (mt) cc_final: 0.9115 (mm) REVERT: D 625 SER cc_start: 0.8794 (m) cc_final: 0.8521 (p) REVERT: D 633 GLN cc_start: 0.8407 (mt0) cc_final: 0.7807 (mp10) REVERT: D 655 ARG cc_start: 0.8729 (mtp85) cc_final: 0.8433 (ttm110) REVERT: D 682 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8372 (mmmm) REVERT: D 740 LEU cc_start: 0.9198 (mt) cc_final: 0.8940 (mt) REVERT: D 868 MET cc_start: 0.8384 (mmm) cc_final: 0.7907 (mmm) REVERT: D 980 ASN cc_start: 0.7986 (t0) cc_final: 0.7395 (m-40) REVERT: D 1071 ARG cc_start: 0.8320 (mtt90) cc_final: 0.8004 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 1039 average time/residue: 0.3913 time to fit residues: 632.3587 Evaluate side-chains 811 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 811 time to evaluate : 3.196 ------------------------------------------------------------------------------- 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: 0.9990 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: 1.9990 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 410 ASN ** 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 D1052 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2424 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= 0.167 Angle : 0.632 12.037 37708 Z= 0.326 Chirality : 0.042 0.225 4248 Planarity : 0.005 0.049 4632 Dihedral : 6.555 48.535 3836 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.54 % Allowed : 16.07 % Favored : 81.39 % 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: -4.25 (0.11), residues: 3232 helix: -2.49 (0.08), residues: 2176 sheet: -2.76 (0.35), residues: 144 loop : -3.12 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 984 HIS 0.012 0.001 HIS D 127 PHE 0.023 0.001 PHE D 969 TYR 0.016 0.001 TYR A 121 ARG 0.004 0.000 ARG D 466 *********************** 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 1065 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 990 time to evaluate : 3.071 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: A 271 GLN cc_start: 0.5924 (tm-30) cc_final: 0.5690 (tm-30) REVERT: A 425 LEU cc_start: 0.9136 (tp) cc_final: 0.8892 (tp) REVERT: A 469 LEU cc_start: 0.9557 (mp) cc_final: 0.8957 (mp) REVERT: A 565 LYS cc_start: 0.8337 (tttp) cc_final: 0.8128 (tptm) REVERT: A 587 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8713 (ttmm) REVERT: A 731 TRP cc_start: 0.8318 (t-100) cc_final: 0.8013 (t-100) REVERT: A 736 TYR cc_start: 0.8707 (t80) cc_final: 0.8279 (t80) REVERT: A 745 TYR cc_start: 0.7506 (t80) cc_final: 0.7137 (t80) REVERT: A 769 LEU cc_start: 0.8333 (tt) cc_final: 0.8112 (tt) REVERT: A 825 ASP cc_start: 0.8543 (t0) cc_final: 0.8284 (t0) REVERT: A 829 PHE cc_start: 0.9151 (m-10) cc_final: 0.8770 (m-10) REVERT: A 856 ASP cc_start: 0.8526 (m-30) cc_final: 0.8207 (m-30) REVERT: A 896 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 980 ASN cc_start: 0.8290 (t0) cc_final: 0.8035 (t0) REVERT: A 1081 ASP cc_start: 0.8711 (t70) cc_final: 0.8404 (t0) REVERT: B 250 HIS cc_start: 0.8782 (m-70) cc_final: 0.8492 (m-70) REVERT: B 565 LYS cc_start: 0.8307 (tttp) cc_final: 0.8014 (tptm) REVERT: B 626 ASN cc_start: 0.7432 (m-40) cc_final: 0.6515 (m-40) REVERT: B 655 ARG cc_start: 0.8741 (mtp85) cc_final: 0.8384 (ttm110) REVERT: B 745 TYR cc_start: 0.7322 (t80) cc_final: 0.6975 (t80) REVERT: B 953 TYR cc_start: 0.7392 (t80) cc_final: 0.6852 (t80) REVERT: B 980 ASN cc_start: 0.8330 (t0) cc_final: 0.8082 (t0) REVERT: B 1071 ARG cc_start: 0.8146 (mtt90) cc_final: 0.7813 (tpp80) REVERT: B 1074 GLN cc_start: 0.8195 (mt0) cc_final: 0.7823 (mp10) REVERT: B 1081 ASP cc_start: 0.8722 (t70) cc_final: 0.8455 (t0) REVERT: C 122 ASP cc_start: 0.5891 (p0) cc_final: 0.5104 (t70) REVERT: C 164 GLN cc_start: 0.8578 (tp40) cc_final: 0.7854 (tp40) REVERT: C 297 GLN cc_start: 0.8994 (pm20) cc_final: 0.8783 (pm20) REVERT: C 460 ASP cc_start: 0.8135 (t0) cc_final: 0.7779 (t70) REVERT: C 655 ARG cc_start: 0.8778 (mtp85) cc_final: 0.8460 (ttm110) REVERT: C 682 LYS cc_start: 0.9056 (mmmm) cc_final: 0.8635 (mmmm) REVERT: C 736 TYR cc_start: 0.8853 (t80) cc_final: 0.8078 (t80) REVERT: C 829 PHE cc_start: 0.9096 (m-10) cc_final: 0.8571 (m-10) REVERT: C 856 ASP cc_start: 0.8423 (m-30) cc_final: 0.8195 (m-30) REVERT: C 963 ASN cc_start: 0.8156 (m-40) cc_final: 0.7939 (m110) REVERT: C 980 ASN cc_start: 0.8294 (t0) cc_final: 0.8081 (t0) REVERT: C 1074 GLN cc_start: 0.8128 (mt0) cc_final: 0.7890 (mp10) REVERT: C 1081 ASP cc_start: 0.8627 (t0) cc_final: 0.8396 (t0) REVERT: D 122 ASP cc_start: 0.5290 (p0) cc_final: 0.4597 (t70) REVERT: D 164 GLN cc_start: 0.8404 (tp40) cc_final: 0.7841 (tp40) REVERT: D 290 ILE cc_start: 0.8934 (mm) cc_final: 0.8531 (tt) REVERT: D 321 GLU cc_start: 0.8495 (pm20) cc_final: 0.8108 (pm20) REVERT: D 371 TRP cc_start: 0.7941 (m100) cc_final: 0.7329 (m100) REVERT: D 469 LEU cc_start: 0.9378 (mp) cc_final: 0.8835 (mp) REVERT: D 477 LYS cc_start: 0.8388 (ttmm) cc_final: 0.8046 (mtmt) REVERT: D 521 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7236 (p0) REVERT: D 569 LYS cc_start: 0.9381 (mmtt) cc_final: 0.9181 (mmtp) REVERT: D 625 SER cc_start: 0.8695 (m) cc_final: 0.8403 (p) REVERT: D 629 ASP cc_start: 0.8308 (m-30) cc_final: 0.7982 (m-30) REVERT: D 633 GLN cc_start: 0.8381 (mt0) cc_final: 0.7615 (mp10) REVERT: D 655 ARG cc_start: 0.8729 (mtp85) cc_final: 0.8445 (ttm110) REVERT: D 656 ASP cc_start: 0.8149 (m-30) cc_final: 0.7822 (m-30) REVERT: D 731 TRP cc_start: 0.8073 (t-100) cc_final: 0.7717 (t-100) REVERT: D 762 LEU cc_start: 0.8303 (mm) cc_final: 0.7697 (tt) REVERT: D 856 ASP cc_start: 0.8519 (m-30) cc_final: 0.8317 (m-30) REVERT: D 980 ASN cc_start: 0.7868 (t0) cc_final: 0.7326 (m-40) outliers start: 75 outliers final: 34 residues processed: 1015 average time/residue: 0.3524 time to fit residues: 573.6996 Evaluate side-chains 889 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 854 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 979 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 858 PHE Chi-restraints excluded: chain B residue 979 ASN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 202 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 chunk 322 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 295 optimal weight: 0.0070 chunk 101 optimal weight: 0.6980 chunk 239 optimal weight: 2.9990 overall best weight: 1.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN A 662 GLN ** A 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 412 HIS ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 882 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 491 ASN C 662 GLN D 248 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 ASN ** D 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 ASN ** D1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27856 Z= 0.306 Angle : 0.683 12.063 37708 Z= 0.347 Chirality : 0.044 0.224 4248 Planarity : 0.005 0.050 4632 Dihedral : 6.522 53.277 3836 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 5.11 % Allowed : 18.27 % Favored : 76.62 % 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: -3.10 (0.13), residues: 3232 helix: -1.51 (0.10), residues: 2184 sheet: -2.70 (0.37), residues: 144 loop : -2.90 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 984 HIS 0.005 0.001 HIS D1070 PHE 0.024 0.002 PHE C 969 TYR 0.016 0.002 TYR D 736 ARG 0.004 0.000 ARG D 110 *********************** 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 1030 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 879 time to evaluate : 2.707 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: A 122 ASP cc_start: 0.6399 (OUTLIER) cc_final: 0.6167 (p0) REVERT: A 425 LEU cc_start: 0.9237 (tp) cc_final: 0.8994 (tp) REVERT: A 460 ASP cc_start: 0.8079 (t0) cc_final: 0.7681 (t70) REVERT: A 469 LEU cc_start: 0.9602 (mp) cc_final: 0.9088 (mp) REVERT: A 507 TYR cc_start: 0.7423 (m-80) cc_final: 0.7170 (m-80) REVERT: A 611 GLU cc_start: 0.8293 (pt0) cc_final: 0.7994 (pt0) REVERT: A 655 ARG cc_start: 0.8809 (mtp-110) cc_final: 0.8532 (ttm110) REVERT: A 731 TRP cc_start: 0.8432 (t-100) cc_final: 0.8136 (t-100) REVERT: A 735 PHE cc_start: 0.8486 (t80) cc_final: 0.8265 (t80) REVERT: A 736 TYR cc_start: 0.8914 (t80) cc_final: 0.8234 (t80) REVERT: A 829 PHE cc_start: 0.9198 (m-10) cc_final: 0.8762 (m-10) REVERT: A 856 ASP cc_start: 0.8678 (m-30) cc_final: 0.8439 (m-30) REVERT: A 953 TYR cc_start: 0.7538 (t80) cc_final: 0.7222 (t80) REVERT: A 980 ASN cc_start: 0.8500 (t0) cc_final: 0.8268 (t0) REVERT: A 1071 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7980 (mmm160) REVERT: A 1074 GLN cc_start: 0.7915 (mp10) cc_final: 0.7433 (mp10) REVERT: A 1081 ASP cc_start: 0.8714 (t70) cc_final: 0.8418 (t0) REVERT: B 469 LEU cc_start: 0.9614 (mp) cc_final: 0.9092 (mp) REVERT: B 599 ILE cc_start: 0.8141 (mm) cc_final: 0.7910 (mm) REVERT: B 613 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6844 (mt-10) REVERT: B 627 ASP cc_start: 0.7275 (t70) cc_final: 0.6889 (t70) REVERT: B 655 ARG cc_start: 0.8749 (mtp85) cc_final: 0.8412 (ttm110) REVERT: B 656 ASP cc_start: 0.8254 (m-30) cc_final: 0.7543 (m-30) REVERT: B 672 GLN cc_start: 0.8658 (tp40) cc_final: 0.8361 (tp40) REVERT: B 682 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8758 (mmmm) REVERT: B 731 TRP cc_start: 0.8416 (t-100) cc_final: 0.8140 (t-100) REVERT: B 745 TYR cc_start: 0.7772 (t80) cc_final: 0.7405 (t80) REVERT: B 825 ASP cc_start: 0.8485 (t0) cc_final: 0.8239 (t0) REVERT: B 953 TYR cc_start: 0.7535 (t80) cc_final: 0.7150 (t80) REVERT: B 980 ASN cc_start: 0.8520 (t0) cc_final: 0.8246 (t0) REVERT: B 1071 ARG cc_start: 0.8148 (mtt90) cc_final: 0.7893 (mmm-85) REVERT: B 1074 GLN cc_start: 0.8323 (mt0) cc_final: 0.7736 (mp10) REVERT: B 1081 ASP cc_start: 0.8739 (t70) cc_final: 0.8504 (t0) REVERT: C 132 THR cc_start: 0.8351 (m) cc_final: 0.8088 (m) REVERT: C 460 ASP cc_start: 0.8226 (t0) cc_final: 0.7917 (t70) REVERT: C 469 LEU cc_start: 0.9629 (mp) cc_final: 0.9247 (mp) REVERT: C 646 ASN cc_start: 0.9080 (p0) cc_final: 0.8805 (p0) REVERT: C 655 ARG cc_start: 0.8765 (mtp85) cc_final: 0.8503 (ttm110) REVERT: C 672 GLN cc_start: 0.8634 (tp40) cc_final: 0.8353 (tp40) REVERT: C 745 TYR cc_start: 0.7767 (t80) cc_final: 0.7412 (t80) REVERT: C 775 ARG cc_start: 0.8504 (ptp-170) cc_final: 0.8272 (mmt180) REVERT: C 856 ASP cc_start: 0.8507 (m-30) cc_final: 0.8302 (m-30) REVERT: C 953 TYR cc_start: 0.7555 (t80) cc_final: 0.7176 (t80) REVERT: C 980 ASN cc_start: 0.8554 (t0) cc_final: 0.8284 (t0) REVERT: C 1074 GLN cc_start: 0.8259 (mt0) cc_final: 0.7973 (mp10) REVERT: D 122 ASP cc_start: 0.6091 (OUTLIER) cc_final: 0.5815 (p0) REVERT: D 164 GLN cc_start: 0.8525 (tp40) cc_final: 0.7831 (tp40) REVERT: D 290 ILE cc_start: 0.9033 (mm) cc_final: 0.8639 (tt) REVERT: D 371 TRP cc_start: 0.7895 (m100) cc_final: 0.7402 (m100) REVERT: D 448 ASP cc_start: 0.7497 (p0) cc_final: 0.7261 (p0) REVERT: D 474 ASN cc_start: 0.7900 (p0) cc_final: 0.6706 (p0) REVERT: D 599 ILE cc_start: 0.7647 (mm) cc_final: 0.7442 (mm) REVERT: D 613 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7128 (mt-10) REVERT: D 629 ASP cc_start: 0.8383 (m-30) cc_final: 0.8030 (m-30) REVERT: D 633 GLN cc_start: 0.8334 (mt0) cc_final: 0.7537 (mp10) REVERT: D 655 ARG cc_start: 0.8848 (mtp85) cc_final: 0.8560 (ttm110) REVERT: D 656 ASP cc_start: 0.8430 (m-30) cc_final: 0.8055 (m-30) REVERT: D 682 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8666 (mmmm) REVERT: D 736 TYR cc_start: 0.8837 (t80) cc_final: 0.8380 (t80) REVERT: D 762 LEU cc_start: 0.8350 (mm) cc_final: 0.7813 (tt) REVERT: D 856 ASP cc_start: 0.8659 (m-30) cc_final: 0.8392 (m-30) REVERT: D 980 ASN cc_start: 0.8205 (t0) cc_final: 0.7584 (m-40) outliers start: 151 outliers final: 97 residues processed: 938 average time/residue: 0.3661 time to fit residues: 559.9814 Evaluate side-chains 921 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 821 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 754 GLU Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 858 PHE Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 749 MET Chi-restraints excluded: chain C residue 761 ILE Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 873 VAL Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 299 optimal weight: 0.4980 chunk 317 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 283 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** 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 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 ASN D 835 HIS D1070 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3463 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= 0.181 Angle : 0.613 12.610 37708 Z= 0.306 Chirality : 0.041 0.216 4248 Planarity : 0.004 0.050 4632 Dihedral : 6.106 57.499 3836 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.28 % Allowed : 22.50 % Favored : 74.22 % 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: -2.40 (0.14), residues: 3232 helix: -0.94 (0.11), residues: 2176 sheet: -2.42 (0.39), residues: 144 loop : -2.76 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 984 HIS 0.003 0.001 HIS D 176 PHE 0.024 0.001 PHE C 969 TYR 0.018 0.001 TYR D 763 ARG 0.003 0.000 ARG C 679 *********************** 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 1018 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 921 time to evaluate : 2.785 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: A 469 LEU cc_start: 0.9566 (mp) cc_final: 0.8995 (mp) REVERT: A 611 GLU cc_start: 0.8303 (pt0) cc_final: 0.7695 (pt0) REVERT: A 613 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7062 (mt-10) REVERT: A 655 ARG cc_start: 0.8727 (mtp-110) cc_final: 0.8419 (ttm110) REVERT: A 656 ASP cc_start: 0.8104 (m-30) cc_final: 0.7755 (m-30) REVERT: A 682 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8675 (mmmm) REVERT: A 731 TRP cc_start: 0.8327 (t-100) cc_final: 0.8002 (t-100) REVERT: A 736 TYR cc_start: 0.8775 (t80) cc_final: 0.8062 (t80) REVERT: A 775 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6506 (tmt170) REVERT: A 829 PHE cc_start: 0.9096 (m-10) cc_final: 0.8659 (m-10) REVERT: A 856 ASP cc_start: 0.8657 (m-30) cc_final: 0.8417 (m-30) REVERT: A 885 ARG cc_start: 0.5945 (mpp-170) cc_final: 0.5540 (ptp-170) REVERT: A 980 ASN cc_start: 0.8450 (t0) cc_final: 0.8146 (t0) REVERT: A 1071 ARG cc_start: 0.8111 (mmm-85) cc_final: 0.7818 (mmm-85) REVERT: A 1074 GLN cc_start: 0.7946 (mp10) cc_final: 0.7477 (mp10) REVERT: A 1081 ASP cc_start: 0.8727 (t70) cc_final: 0.8440 (t0) REVERT: B 312 LYS cc_start: 0.8055 (pttp) cc_final: 0.7570 (mmmt) REVERT: B 351 ARG cc_start: 0.6747 (ttp-110) cc_final: 0.6384 (ptp90) REVERT: B 469 LEU cc_start: 0.9550 (mp) cc_final: 0.8963 (mp) REVERT: B 592 MET cc_start: 0.8552 (mtp) cc_final: 0.8270 (ttm) REVERT: B 613 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7009 (mt-10) REVERT: B 622 GLU cc_start: 0.7461 (tp30) cc_final: 0.7037 (tp30) REVERT: B 626 ASN cc_start: 0.8326 (m-40) cc_final: 0.8078 (m-40) REVERT: B 627 ASP cc_start: 0.7313 (t70) cc_final: 0.6923 (t70) REVERT: B 656 ASP cc_start: 0.8148 (m-30) cc_final: 0.7553 (m-30) REVERT: B 672 GLN cc_start: 0.8570 (tp40) cc_final: 0.8287 (tp40) REVERT: B 745 TYR cc_start: 0.7665 (t80) cc_final: 0.7294 (t80) REVERT: B 749 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7597 (mmp) REVERT: B 825 ASP cc_start: 0.8418 (t0) cc_final: 0.8188 (t0) REVERT: B 899 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6485 (pp) REVERT: B 980 ASN cc_start: 0.8506 (t0) cc_final: 0.8201 (t0) REVERT: B 1071 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7743 (mmm-85) REVERT: B 1074 GLN cc_start: 0.8292 (mt0) cc_final: 0.7816 (mp10) REVERT: B 1081 ASP cc_start: 0.8811 (t70) cc_final: 0.8550 (t0) REVERT: C 435 ASP cc_start: 0.8155 (m-30) cc_final: 0.7954 (m-30) REVERT: C 469 LEU cc_start: 0.9588 (mp) cc_final: 0.9089 (mp) REVERT: C 587 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8649 (ttmm) REVERT: C 622 GLU cc_start: 0.7398 (tp30) cc_final: 0.6971 (tp30) REVERT: C 627 ASP cc_start: 0.7210 (t70) cc_final: 0.6757 (t70) REVERT: C 646 ASN cc_start: 0.8992 (p0) cc_final: 0.8732 (p0) REVERT: C 655 ARG cc_start: 0.8738 (mtp85) cc_final: 0.8535 (ttm110) REVERT: C 672 GLN cc_start: 0.8531 (tp40) cc_final: 0.8247 (tp40) REVERT: C 731 TRP cc_start: 0.8308 (t-100) cc_final: 0.8006 (t-100) REVERT: C 745 TYR cc_start: 0.7734 (t80) cc_final: 0.7353 (t80) REVERT: C 749 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7641 (mmp) REVERT: C 856 ASP cc_start: 0.8499 (m-30) cc_final: 0.8287 (m-30) REVERT: C 980 ASN cc_start: 0.8508 (t0) cc_final: 0.8281 (t0) REVERT: C 1074 GLN cc_start: 0.8267 (mt0) cc_final: 0.8005 (mp10) REVERT: D 371 TRP cc_start: 0.7845 (m100) cc_final: 0.7530 (m100) REVERT: D 498 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7901 (mmtt) REVERT: D 565 LYS cc_start: 0.8591 (tttp) cc_final: 0.8387 (tptm) REVERT: D 599 ILE cc_start: 0.7660 (mm) cc_final: 0.7405 (mm) REVERT: D 625 SER cc_start: 0.8658 (m) cc_final: 0.8380 (p) REVERT: D 629 ASP cc_start: 0.8341 (m-30) cc_final: 0.7949 (m-30) REVERT: D 633 GLN cc_start: 0.8311 (mt0) cc_final: 0.7483 (mp10) REVERT: D 655 ARG cc_start: 0.8802 (mtp85) cc_final: 0.8589 (ttm110) REVERT: D 736 TYR cc_start: 0.8819 (t80) cc_final: 0.8213 (t80) REVERT: D 856 ASP cc_start: 0.8673 (m-30) cc_final: 0.8463 (m-30) REVERT: D 980 ASN cc_start: 0.8244 (t0) cc_final: 0.7673 (m-40) outliers start: 97 outliers final: 66 residues processed: 958 average time/residue: 0.3539 time to fit residues: 550.3149 Evaluate side-chains 912 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 841 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 858 PHE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 749 MET Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 618 GLU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 688 MET Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 0.0070 chunk 179 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 236 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 270 optimal weight: 0.9980 chunk 219 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 80 optimal weight: 0.0970 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 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 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 979 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 835 HIS D1070 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27856 Z= 0.165 Angle : 0.613 12.956 37708 Z= 0.301 Chirality : 0.041 0.227 4248 Planarity : 0.004 0.053 4632 Dihedral : 5.930 59.828 3836 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.42 % Allowed : 24.36 % Favored : 72.23 % 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: -1.97 (0.14), residues: 3232 helix: -0.60 (0.11), residues: 2176 sheet: -2.21 (0.40), residues: 144 loop : -2.67 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 984 HIS 0.005 0.001 HIS B 380 PHE 0.027 0.001 PHE D 969 TYR 0.018 0.001 TYR D 763 ARG 0.003 0.000 ARG B 355 *********************** 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 999 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 898 time to evaluate : 2.738 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: A 312 LYS cc_start: 0.8073 (pttp) cc_final: 0.7571 (mmmt) REVERT: A 469 LEU cc_start: 0.9525 (mp) cc_final: 0.8927 (mp) REVERT: A 498 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7498 (mmtp) REVERT: A 622 GLU cc_start: 0.7502 (tp30) cc_final: 0.7285 (tp30) REVERT: A 655 ARG cc_start: 0.8712 (mtp-110) cc_final: 0.8397 (ttm110) REVERT: A 656 ASP cc_start: 0.7962 (m-30) cc_final: 0.7728 (m-30) REVERT: A 682 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8752 (mmmm) REVERT: A 736 TYR cc_start: 0.8816 (t80) cc_final: 0.7974 (t80) REVERT: A 771 CYS cc_start: 0.7208 (p) cc_final: 0.6978 (p) REVERT: A 775 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6561 (tmt170) REVERT: A 829 PHE cc_start: 0.9077 (m-10) cc_final: 0.8606 (m-10) REVERT: A 856 ASP cc_start: 0.8620 (m-30) cc_final: 0.8388 (m-30) REVERT: A 899 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6436 (pp) REVERT: A 953 TYR cc_start: 0.7380 (t80) cc_final: 0.7127 (t80) REVERT: A 980 ASN cc_start: 0.8411 (t0) cc_final: 0.8107 (t0) REVERT: A 1071 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7746 (mmm-85) REVERT: A 1074 GLN cc_start: 0.7992 (mp10) cc_final: 0.7504 (mp10) REVERT: A 1081 ASP cc_start: 0.8724 (t70) cc_final: 0.8477 (t0) REVERT: B 351 ARG cc_start: 0.6853 (ttp-110) cc_final: 0.6556 (ptp90) REVERT: B 469 LEU cc_start: 0.9529 (mp) cc_final: 0.8931 (mp) REVERT: B 474 ASN cc_start: 0.7288 (p0) cc_final: 0.7028 (p0) REVERT: B 565 LYS cc_start: 0.8354 (tttp) cc_final: 0.8072 (tptm) REVERT: B 613 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7202 (mt-10) REVERT: B 622 GLU cc_start: 0.7433 (tp30) cc_final: 0.7056 (tp30) REVERT: B 627 ASP cc_start: 0.7287 (t70) cc_final: 0.6920 (t70) REVERT: B 655 ARG cc_start: 0.8667 (mtp-110) cc_final: 0.8367 (ttm110) REVERT: B 672 GLN cc_start: 0.8560 (tp40) cc_final: 0.8285 (tp40) REVERT: B 682 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8625 (mmmm) REVERT: B 745 TYR cc_start: 0.7659 (t80) cc_final: 0.7380 (t80) REVERT: B 899 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6498 (pp) REVERT: B 980 ASN cc_start: 0.8507 (t0) cc_final: 0.8211 (t0) REVERT: B 1081 ASP cc_start: 0.8839 (t70) cc_final: 0.8599 (t0) REVERT: C 469 LEU cc_start: 0.9547 (mp) cc_final: 0.8989 (mp) REVERT: C 498 LYS cc_start: 0.8196 (mmtp) cc_final: 0.7546 (mmtp) REVERT: C 587 LYS cc_start: 0.8871 (ttmm) cc_final: 0.8567 (ttmm) REVERT: C 613 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7608 (mt-10) REVERT: C 622 GLU cc_start: 0.7419 (tp30) cc_final: 0.7068 (tp30) REVERT: C 627 ASP cc_start: 0.7241 (t70) cc_final: 0.6728 (t70) REVERT: C 646 ASN cc_start: 0.8956 (p0) cc_final: 0.8681 (p0) REVERT: C 655 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8501 (ttm110) REVERT: C 669 LEU cc_start: 0.9033 (tp) cc_final: 0.8750 (tp) REVERT: C 672 GLN cc_start: 0.8506 (tp40) cc_final: 0.8227 (tp40) REVERT: C 682 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8615 (mmmm) REVERT: C 745 TYR cc_start: 0.7603 (t80) cc_final: 0.7229 (t80) REVERT: C 804 ILE cc_start: 0.7766 (mm) cc_final: 0.7073 (mm) REVERT: C 899 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6354 (pp) REVERT: C 980 ASN cc_start: 0.8506 (t0) cc_final: 0.8232 (t0) REVERT: C 1074 GLN cc_start: 0.8276 (mt0) cc_final: 0.7989 (mp10) REVERT: D 434 SER cc_start: 0.9100 (t) cc_final: 0.8845 (p) REVERT: D 435 ASP cc_start: 0.8124 (m-30) cc_final: 0.7895 (m-30) REVERT: D 448 ASP cc_start: 0.7257 (p0) cc_final: 0.6997 (p0) REVERT: D 469 LEU cc_start: 0.9532 (mp) cc_final: 0.9075 (mp) REVERT: D 474 ASN cc_start: 0.7825 (p0) cc_final: 0.7624 (p0) REVERT: D 498 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7880 (mmtt) REVERT: D 565 LYS cc_start: 0.8544 (tttp) cc_final: 0.8336 (tptm) REVERT: D 613 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7236 (mt-10) REVERT: D 622 GLU cc_start: 0.7560 (tp30) cc_final: 0.6943 (tp30) REVERT: D 629 ASP cc_start: 0.8335 (m-30) cc_final: 0.7990 (m-30) REVERT: D 633 GLN cc_start: 0.8359 (mt0) cc_final: 0.7527 (mp10) REVERT: D 656 ASP cc_start: 0.8163 (m-30) cc_final: 0.7773 (m-30) REVERT: D 682 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8419 (mmmm) REVERT: D 736 TYR cc_start: 0.8827 (t80) cc_final: 0.8132 (t80) REVERT: D 980 ASN cc_start: 0.8302 (t0) cc_final: 0.7651 (m-40) outliers start: 101 outliers final: 74 residues processed: 942 average time/residue: 0.3521 time to fit residues: 533.3831 Evaluate side-chains 931 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 851 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 858 PHE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 979 ASN Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 688 MET Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 0.6980 chunk 285 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 186 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 263 optimal weight: 0.0010 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 chunk 166 optimal weight: 0.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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 ** 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 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1070 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 27856 Z= 0.158 Angle : 0.613 13.157 37708 Z= 0.300 Chirality : 0.041 0.328 4248 Planarity : 0.004 0.055 4632 Dihedral : 5.775 58.598 3836 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.48 % Allowed : 25.27 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3232 helix: -0.35 (0.11), residues: 2180 sheet: -1.92 (0.41), residues: 144 loop : -2.60 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 984 HIS 0.008 0.001 HIS D1070 PHE 0.027 0.001 PHE D 969 TYR 0.020 0.001 TYR D 763 ARG 0.006 0.000 ARG D 655 *********************** 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 994 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 891 time to evaluate : 3.157 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: A 312 LYS cc_start: 0.8059 (pttp) cc_final: 0.7546 (mmmt) REVERT: A 469 LEU cc_start: 0.9490 (mp) cc_final: 0.8916 (mp) REVERT: A 474 ASN cc_start: 0.7321 (p0) cc_final: 0.6735 (p0) REVERT: A 498 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7454 (mmtp) REVERT: A 613 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6984 (mt-10) REVERT: A 622 GLU cc_start: 0.7604 (tp30) cc_final: 0.7226 (tp30) REVERT: A 655 ARG cc_start: 0.8703 (mtp-110) cc_final: 0.8267 (ttm110) REVERT: A 669 LEU cc_start: 0.9280 (mt) cc_final: 0.9046 (mp) REVERT: A 682 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8722 (mmmm) REVERT: A 736 TYR cc_start: 0.8821 (t80) cc_final: 0.7963 (t80) REVERT: A 825 ASP cc_start: 0.8470 (t0) cc_final: 0.8230 (t0) REVERT: A 856 ASP cc_start: 0.8583 (m-30) cc_final: 0.8347 (m-30) REVERT: A 953 TYR cc_start: 0.7372 (t80) cc_final: 0.7096 (t80) REVERT: A 980 ASN cc_start: 0.8441 (t0) cc_final: 0.8115 (t0) REVERT: A 1071 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7672 (mmm-85) REVERT: A 1074 GLN cc_start: 0.8004 (mp10) cc_final: 0.7557 (mp10) REVERT: B 366 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8033 (mm-30) REVERT: B 469 LEU cc_start: 0.9495 (mp) cc_final: 0.8930 (mp) REVERT: B 565 LYS cc_start: 0.8293 (tttp) cc_final: 0.7976 (tptm) REVERT: B 622 GLU cc_start: 0.7491 (tp30) cc_final: 0.7017 (tp30) REVERT: B 627 ASP cc_start: 0.7270 (t70) cc_final: 0.6894 (t70) REVERT: B 672 GLN cc_start: 0.8524 (tp40) cc_final: 0.8219 (tp40) REVERT: B 682 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8578 (mmmm) REVERT: B 736 TYR cc_start: 0.8882 (t80) cc_final: 0.8153 (t80) REVERT: B 745 TYR cc_start: 0.7609 (t80) cc_final: 0.7360 (t80) REVERT: B 829 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8194 (m-10) REVERT: B 899 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6525 (pp) REVERT: B 969 PHE cc_start: 0.8135 (m-80) cc_final: 0.7827 (m-80) REVERT: B 980 ASN cc_start: 0.8526 (t0) cc_final: 0.8230 (t0) REVERT: B 1074 GLN cc_start: 0.8196 (mt0) cc_final: 0.7875 (mp10) REVERT: B 1081 ASP cc_start: 0.8850 (t70) cc_final: 0.8625 (t0) REVERT: C 469 LEU cc_start: 0.9547 (mp) cc_final: 0.8971 (mp) REVERT: C 498 LYS cc_start: 0.8131 (mmtp) cc_final: 0.7401 (mmtp) REVERT: C 587 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8490 (ttmm) REVERT: C 612 TYR cc_start: 0.9171 (m-80) cc_final: 0.8757 (m-80) REVERT: C 622 GLU cc_start: 0.7440 (tp30) cc_final: 0.7004 (tp30) REVERT: C 627 ASP cc_start: 0.7202 (t70) cc_final: 0.6777 (t70) REVERT: C 655 ARG cc_start: 0.8685 (mtp85) cc_final: 0.8481 (ttm110) REVERT: C 669 LEU cc_start: 0.9003 (tp) cc_final: 0.8736 (tp) REVERT: C 672 GLN cc_start: 0.8482 (tp40) cc_final: 0.8206 (tp40) REVERT: C 682 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8627 (mmmm) REVERT: C 736 TYR cc_start: 0.8881 (t80) cc_final: 0.8098 (t80) REVERT: C 745 TYR cc_start: 0.7531 (t80) cc_final: 0.7291 (t80) REVERT: C 775 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6354 (tmt170) REVERT: C 899 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6289 (pp) REVERT: C 980 ASN cc_start: 0.8588 (t0) cc_final: 0.8332 (t0) REVERT: C 1074 GLN cc_start: 0.8240 (mt0) cc_final: 0.7971 (mp10) REVERT: D 434 SER cc_start: 0.9062 (t) cc_final: 0.8836 (p) REVERT: D 469 LEU cc_start: 0.9511 (mp) cc_final: 0.9038 (mp) REVERT: D 474 ASN cc_start: 0.7859 (p0) cc_final: 0.7625 (p0) REVERT: D 498 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7870 (mmtt) REVERT: D 565 LYS cc_start: 0.8499 (tttp) cc_final: 0.8256 (tptm) REVERT: D 613 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7151 (mt-10) REVERT: D 622 GLU cc_start: 0.7621 (tp30) cc_final: 0.7253 (tp30) REVERT: D 629 ASP cc_start: 0.8344 (m-30) cc_final: 0.7982 (m-30) REVERT: D 633 GLN cc_start: 0.8390 (mt0) cc_final: 0.7573 (mp10) REVERT: D 656 ASP cc_start: 0.8335 (m-30) cc_final: 0.7922 (m-30) REVERT: D 682 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8456 (mmmm) REVERT: D 731 TRP cc_start: 0.8292 (t-100) cc_final: 0.8002 (t-100) REVERT: D 736 TYR cc_start: 0.8848 (t80) cc_final: 0.8136 (t80) REVERT: D 980 ASN cc_start: 0.8290 (t0) cc_final: 0.7494 (m-40) REVERT: D 1049 MET cc_start: 0.8662 (ptm) cc_final: 0.8418 (ttp) outliers start: 103 outliers final: 72 residues processed: 938 average time/residue: 0.3497 time to fit residues: 528.2990 Evaluate side-chains 930 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 851 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 829 PHE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 618 GLU Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 688 MET Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 231 optimal weight: 0.5980 chunk 179 optimal weight: 0.0870 chunk 267 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 316 optimal weight: 0.1980 chunk 197 optimal weight: 4.9990 chunk 192 optimal weight: 0.5980 chunk 145 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN B 474 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 HIS ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN C 420 GLN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 835 HIS ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 835 HIS D1070 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27856 Z= 0.163 Angle : 0.617 13.241 37708 Z= 0.302 Chirality : 0.042 0.530 4248 Planarity : 0.004 0.057 4632 Dihedral : 5.678 58.698 3836 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.69 % Allowed : 25.61 % Favored : 70.70 % 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: -1.36 (0.14), residues: 3232 helix: -0.12 (0.11), residues: 2164 sheet: -1.65 (0.43), residues: 144 loop : -2.51 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 984 HIS 0.011 0.001 HIS D1070 PHE 0.031 0.001 PHE D 969 TYR 0.018 0.001 TYR D 763 ARG 0.008 0.000 ARG B 655 *********************** 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 993 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 884 time to evaluate : 2.845 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: A 271 GLN cc_start: 0.6690 (tm-30) cc_final: 0.6320 (tm-30) REVERT: A 469 LEU cc_start: 0.9504 (mp) cc_final: 0.8936 (mp) REVERT: A 498 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7481 (mmtp) REVERT: A 622 GLU cc_start: 0.7569 (tp30) cc_final: 0.7135 (tp30) REVERT: A 655 ARG cc_start: 0.8604 (mtp-110) cc_final: 0.8285 (ttm110) REVERT: A 682 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8721 (mmmm) REVERT: A 856 ASP cc_start: 0.8509 (m-30) cc_final: 0.8281 (m-30) REVERT: A 899 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6305 (pp) REVERT: A 980 ASN cc_start: 0.8419 (t0) cc_final: 0.8095 (t0) REVERT: A 1071 ARG cc_start: 0.8062 (mmm-85) cc_final: 0.7627 (mmm-85) REVERT: A 1074 GLN cc_start: 0.8006 (mp10) cc_final: 0.7574 (mp10) REVERT: B 469 LEU cc_start: 0.9497 (mp) cc_final: 0.8920 (mp) REVERT: B 565 LYS cc_start: 0.8279 (tttp) cc_final: 0.7944 (tptm) REVERT: B 622 GLU cc_start: 0.7494 (tp30) cc_final: 0.7048 (tp30) REVERT: B 627 ASP cc_start: 0.7228 (t70) cc_final: 0.6873 (t70) REVERT: B 672 GLN cc_start: 0.8515 (tp40) cc_final: 0.8227 (tp40) REVERT: B 682 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8571 (mmmm) REVERT: B 736 TYR cc_start: 0.8905 (t80) cc_final: 0.8162 (t80) REVERT: B 745 TYR cc_start: 0.7598 (t80) cc_final: 0.7346 (t80) REVERT: B 829 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8188 (m-10) REVERT: B 899 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6545 (pp) REVERT: B 969 PHE cc_start: 0.8078 (m-80) cc_final: 0.7860 (m-80) REVERT: B 980 ASN cc_start: 0.8485 (t0) cc_final: 0.8169 (t0) REVERT: B 1081 ASP cc_start: 0.8871 (t70) cc_final: 0.8646 (t0) REVERT: C 250 HIS cc_start: 0.8688 (m-70) cc_final: 0.8419 (m-70) REVERT: C 312 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7828 (pttp) REVERT: C 469 LEU cc_start: 0.9496 (mp) cc_final: 0.8886 (mp) REVERT: C 498 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7423 (mmtp) REVERT: C 587 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8422 (ttmm) REVERT: C 613 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6894 (tp30) REVERT: C 622 GLU cc_start: 0.7414 (tp30) cc_final: 0.7009 (tp30) REVERT: C 627 ASP cc_start: 0.7217 (t70) cc_final: 0.6728 (t70) REVERT: C 655 ARG cc_start: 0.8542 (mtp85) cc_final: 0.8206 (ttm110) REVERT: C 656 ASP cc_start: 0.8124 (m-30) cc_final: 0.6898 (m-30) REVERT: C 669 LEU cc_start: 0.8989 (tp) cc_final: 0.8744 (tp) REVERT: C 672 GLN cc_start: 0.8483 (tp40) cc_final: 0.8238 (tp40) REVERT: C 682 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8604 (mmmm) REVERT: C 736 TYR cc_start: 0.8932 (t80) cc_final: 0.8166 (t80) REVERT: C 745 TYR cc_start: 0.7511 (t80) cc_final: 0.7291 (t80) REVERT: C 775 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6391 (tmt170) REVERT: C 899 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6272 (pp) REVERT: C 953 TYR cc_start: 0.7297 (t80) cc_final: 0.7077 (t80) REVERT: C 980 ASN cc_start: 0.8596 (t0) cc_final: 0.8325 (t0) REVERT: C 1070 HIS cc_start: 0.7583 (p-80) cc_final: 0.6663 (t70) REVERT: D 164 GLN cc_start: 0.8384 (tp40) cc_final: 0.7718 (tp40) REVERT: D 469 LEU cc_start: 0.9512 (mp) cc_final: 0.9003 (mp) REVERT: D 474 ASN cc_start: 0.7808 (p0) cc_final: 0.7574 (p0) REVERT: D 498 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7823 (mmtt) REVERT: D 613 GLU cc_start: 0.7766 (mt-10) cc_final: 0.6947 (mt-10) REVERT: D 622 GLU cc_start: 0.7569 (tp30) cc_final: 0.7161 (tp30) REVERT: D 629 ASP cc_start: 0.8430 (m-30) cc_final: 0.8043 (m-30) REVERT: D 633 GLN cc_start: 0.8401 (mt0) cc_final: 0.7577 (mp10) REVERT: D 656 ASP cc_start: 0.8309 (m-30) cc_final: 0.7622 (m-30) REVERT: D 731 TRP cc_start: 0.8273 (t-100) cc_final: 0.7985 (t-100) REVERT: D 980 ASN cc_start: 0.8269 (t0) cc_final: 0.7523 (m110) REVERT: D 1049 MET cc_start: 0.8679 (ptm) cc_final: 0.8363 (ttp) outliers start: 109 outliers final: 83 residues processed: 935 average time/residue: 0.3531 time to fit residues: 530.4824 Evaluate side-chains 937 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 846 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 829 PHE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 688 MET Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 0.0570 chunk 126 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 156 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 chunk 248 optimal weight: 0.6980 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN C 563 ASN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 776 GLN D1052 ASN D1070 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27856 Z= 0.167 Angle : 0.630 13.147 37708 Z= 0.308 Chirality : 0.042 0.240 4248 Planarity : 0.004 0.056 4632 Dihedral : 5.618 59.256 3836 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.72 % Allowed : 25.95 % Favored : 70.33 % 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: -1.11 (0.15), residues: 3232 helix: 0.11 (0.11), residues: 2140 sheet: -1.46 (0.43), residues: 144 loop : -2.49 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 984 HIS 0.009 0.001 HIS D1070 PHE 0.031 0.001 PHE D 969 TYR 0.017 0.001 TYR D 763 ARG 0.007 0.000 ARG B 655 *********************** 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 977 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 867 time to evaluate : 2.950 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: A 271 GLN cc_start: 0.6836 (tm-30) cc_final: 0.6464 (tm-30) REVERT: A 465 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 469 LEU cc_start: 0.9497 (mp) cc_final: 0.8926 (mp) REVERT: A 498 LYS cc_start: 0.8180 (mmtp) cc_final: 0.7448 (mmtp) REVERT: A 622 GLU cc_start: 0.7599 (tp30) cc_final: 0.7139 (tp30) REVERT: A 655 ARG cc_start: 0.8579 (mtp-110) cc_final: 0.8141 (ttm110) REVERT: A 669 LEU cc_start: 0.9286 (mt) cc_final: 0.9032 (mp) REVERT: A 682 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8643 (mmmm) REVERT: A 742 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7543 (tp) REVERT: A 825 ASP cc_start: 0.8417 (t0) cc_final: 0.8174 (t0) REVERT: A 856 ASP cc_start: 0.8507 (m-30) cc_final: 0.8255 (m-30) REVERT: A 899 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6480 (pp) REVERT: A 980 ASN cc_start: 0.8437 (t0) cc_final: 0.8128 (t0) REVERT: A 1070 HIS cc_start: 0.7948 (OUTLIER) cc_final: 0.7010 (t-170) REVERT: A 1071 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7525 (mmm-85) REVERT: B 366 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8033 (mm-30) REVERT: B 469 LEU cc_start: 0.9503 (mp) cc_final: 0.8931 (mp) REVERT: B 565 LYS cc_start: 0.8258 (tttp) cc_final: 0.7788 (tptm) REVERT: B 587 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8583 (ttmm) REVERT: B 622 GLU cc_start: 0.7458 (tp30) cc_final: 0.7018 (tp30) REVERT: B 672 GLN cc_start: 0.8536 (tp40) cc_final: 0.8216 (tp40) REVERT: B 682 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8547 (mmmm) REVERT: B 736 TYR cc_start: 0.8933 (t80) cc_final: 0.8262 (t80) REVERT: B 745 TYR cc_start: 0.7548 (t80) cc_final: 0.7326 (t80) REVERT: B 829 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8312 (m-10) REVERT: B 899 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6357 (pp) REVERT: B 953 TYR cc_start: 0.7362 (t80) cc_final: 0.7063 (t80) REVERT: B 980 ASN cc_start: 0.8479 (t0) cc_final: 0.8167 (t0) REVERT: B 1070 HIS cc_start: 0.7880 (p-80) cc_final: 0.7248 (t70) REVERT: B 1081 ASP cc_start: 0.8866 (t70) cc_final: 0.8606 (t0) REVERT: C 250 HIS cc_start: 0.8688 (m-70) cc_final: 0.8417 (m-70) REVERT: C 469 LEU cc_start: 0.9433 (mp) cc_final: 0.8838 (mp) REVERT: C 498 LYS cc_start: 0.8200 (mmtp) cc_final: 0.7441 (mmtp) REVERT: C 622 GLU cc_start: 0.7404 (tp30) cc_final: 0.7008 (tp30) REVERT: C 627 ASP cc_start: 0.7208 (t70) cc_final: 0.6757 (t70) REVERT: C 655 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8264 (ttm110) REVERT: C 672 GLN cc_start: 0.8504 (tp40) cc_final: 0.8254 (tp40) REVERT: C 682 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8590 (mmmm) REVERT: C 731 TRP cc_start: 0.8266 (t-100) cc_final: 0.8037 (t-100) REVERT: C 736 TYR cc_start: 0.9009 (t80) cc_final: 0.8314 (t80) REVERT: C 745 TYR cc_start: 0.7564 (t80) cc_final: 0.7324 (t80) REVERT: C 775 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6465 (tmt170) REVERT: C 899 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6274 (pp) REVERT: C 953 TYR cc_start: 0.7321 (t80) cc_final: 0.7093 (t80) REVERT: C 980 ASN cc_start: 0.8585 (t0) cc_final: 0.8294 (t0) REVERT: C 1074 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: D 289 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7852 (mmmt) REVERT: D 469 LEU cc_start: 0.9510 (mp) cc_final: 0.9001 (mp) REVERT: D 474 ASN cc_start: 0.7820 (p0) cc_final: 0.7601 (p0) REVERT: D 498 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7788 (mmtt) REVERT: D 592 MET cc_start: 0.8662 (mtp) cc_final: 0.8354 (ttm) REVERT: D 613 GLU cc_start: 0.7805 (mt-10) cc_final: 0.6912 (mt-10) REVERT: D 622 GLU cc_start: 0.7531 (tp30) cc_final: 0.7162 (tp30) REVERT: D 629 ASP cc_start: 0.8381 (m-30) cc_final: 0.8000 (m-30) REVERT: D 633 GLN cc_start: 0.8404 (mt0) cc_final: 0.7587 (mp10) REVERT: D 656 ASP cc_start: 0.8396 (m-30) cc_final: 0.7675 (m-30) REVERT: D 682 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8348 (mmmm) REVERT: D 731 TRP cc_start: 0.8239 (t-100) cc_final: 0.7943 (t-100) REVERT: D 736 TYR cc_start: 0.8931 (t80) cc_final: 0.8250 (t80) REVERT: D 980 ASN cc_start: 0.8281 (t0) cc_final: 0.7650 (m-40) REVERT: D 1049 MET cc_start: 0.8715 (ptm) cc_final: 0.8337 (ttp) REVERT: D 1070 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.7814 (t70) outliers start: 110 outliers final: 86 residues processed: 920 average time/residue: 0.3515 time to fit residues: 520.8423 Evaluate side-chains 940 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 841 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 829 PHE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 1074 GLN Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 688 MET Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 0.9980 chunk 302 optimal weight: 4.9990 chunk 276 optimal weight: 0.0870 chunk 294 optimal weight: 0.7980 chunk 177 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 chunk 231 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 278 optimal weight: 0.0770 chunk 293 optimal weight: 0.9980 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 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 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 HIS ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27856 Z= 0.172 Angle : 0.643 13.191 37708 Z= 0.313 Chirality : 0.041 0.252 4248 Planarity : 0.004 0.056 4632 Dihedral : 5.615 59.608 3836 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.45 % Allowed : 26.42 % Favored : 70.13 % Cbeta Deviations : 0.06 % 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: -0.93 (0.15), residues: 3232 helix: 0.27 (0.11), residues: 2124 sheet: -1.33 (0.44), residues: 144 loop : -2.43 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 984 HIS 0.007 0.001 HIS D1070 PHE 0.032 0.001 PHE D 969 TYR 0.018 0.001 TYR C 895 ARG 0.008 0.000 ARG B 655 *********************** 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 968 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 866 time to evaluate : 2.962 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: A 465 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.8848 (p) REVERT: A 469 LEU cc_start: 0.9495 (mp) cc_final: 0.8921 (mp) REVERT: A 498 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7282 (mmtp) REVERT: A 622 GLU cc_start: 0.7583 (tp30) cc_final: 0.7111 (tp30) REVERT: A 655 ARG cc_start: 0.8556 (mtp-110) cc_final: 0.8341 (ttm110) REVERT: A 669 LEU cc_start: 0.9297 (mt) cc_final: 0.9033 (mp) REVERT: A 682 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8635 (mmmm) REVERT: A 742 LEU cc_start: 0.7923 (tp) cc_final: 0.7522 (tp) REVERT: A 856 ASP cc_start: 0.8504 (m-30) cc_final: 0.8257 (m-30) REVERT: A 899 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6487 (pp) REVERT: A 980 ASN cc_start: 0.8407 (t0) cc_final: 0.8060 (t0) REVERT: A 1071 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7867 (mmm-85) REVERT: B 250 HIS cc_start: 0.8583 (m-70) cc_final: 0.8267 (m-70) REVERT: B 366 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8033 (mm-30) REVERT: B 469 LEU cc_start: 0.9484 (mp) cc_final: 0.8907 (mp) REVERT: B 587 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8567 (ttmm) REVERT: B 612 TYR cc_start: 0.9129 (m-80) cc_final: 0.8731 (m-80) REVERT: B 613 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7198 (tp30) REVERT: B 672 GLN cc_start: 0.8472 (tp40) cc_final: 0.8137 (tp40) REVERT: B 682 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8537 (mmmm) REVERT: B 736 TYR cc_start: 0.8944 (t80) cc_final: 0.8250 (t80) REVERT: B 742 LEU cc_start: 0.7978 (tp) cc_final: 0.7561 (tp) REVERT: B 745 TYR cc_start: 0.7566 (t80) cc_final: 0.7356 (t80) REVERT: B 829 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8287 (m-10) REVERT: B 858 PHE cc_start: 0.8246 (t80) cc_final: 0.7895 (t80) REVERT: B 899 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6320 (pp) REVERT: B 953 TYR cc_start: 0.7333 (t80) cc_final: 0.7059 (t80) REVERT: B 980 ASN cc_start: 0.8483 (t0) cc_final: 0.8140 (t0) REVERT: B 1070 HIS cc_start: 0.7880 (p-80) cc_final: 0.7275 (t70) REVERT: B 1081 ASP cc_start: 0.8854 (t70) cc_final: 0.8596 (t0) REVERT: C 250 HIS cc_start: 0.8636 (m-70) cc_final: 0.8367 (m-70) REVERT: C 469 LEU cc_start: 0.9428 (mp) cc_final: 0.8817 (mp) REVERT: C 498 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7380 (mmtp) REVERT: C 612 TYR cc_start: 0.9131 (m-80) cc_final: 0.8690 (m-80) REVERT: C 613 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: C 622 GLU cc_start: 0.7395 (tp30) cc_final: 0.7021 (tp30) REVERT: C 656 ASP cc_start: 0.7629 (m-30) cc_final: 0.7089 (m-30) REVERT: C 672 GLN cc_start: 0.8506 (tp40) cc_final: 0.8282 (tp40) REVERT: C 682 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8647 (mmmm) REVERT: C 736 TYR cc_start: 0.8996 (t80) cc_final: 0.8298 (t80) REVERT: C 742 LEU cc_start: 0.7833 (tp) cc_final: 0.7609 (tp) REVERT: C 745 TYR cc_start: 0.7580 (t80) cc_final: 0.7373 (t80) REVERT: C 775 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6392 (tmt170) REVERT: C 899 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6298 (pp) REVERT: C 953 TYR cc_start: 0.7335 (t80) cc_final: 0.7134 (t80) REVERT: C 980 ASN cc_start: 0.8575 (t0) cc_final: 0.8285 (t0) REVERT: C 1074 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: D 469 LEU cc_start: 0.9514 (mp) cc_final: 0.9003 (mp) REVERT: D 474 ASN cc_start: 0.7834 (p0) cc_final: 0.7626 (p0) REVERT: D 498 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7788 (mmtt) REVERT: D 592 MET cc_start: 0.8649 (mtp) cc_final: 0.8382 (ttm) REVERT: D 613 GLU cc_start: 0.7859 (mt-10) cc_final: 0.6952 (mt-10) REVERT: D 622 GLU cc_start: 0.7496 (tp30) cc_final: 0.7100 (tp30) REVERT: D 629 ASP cc_start: 0.8371 (m-30) cc_final: 0.8003 (m-30) REVERT: D 633 GLN cc_start: 0.8415 (mt0) cc_final: 0.7583 (mp10) REVERT: D 656 ASP cc_start: 0.8539 (m-30) cc_final: 0.7762 (m-30) REVERT: D 731 TRP cc_start: 0.8232 (t-100) cc_final: 0.7911 (t-100) REVERT: D 736 TYR cc_start: 0.8941 (t80) cc_final: 0.8291 (t80) REVERT: D 980 ASN cc_start: 0.8287 (t0) cc_final: 0.7664 (m-40) REVERT: D 1049 MET cc_start: 0.8731 (ptm) cc_final: 0.8490 (ptm) outliers start: 102 outliers final: 82 residues processed: 906 average time/residue: 0.3396 time to fit residues: 500.2540 Evaluate side-chains 937 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 844 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 829 PHE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 1074 GLN Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 618 GLU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 688 MET Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 990 PHE Chi-restraints excluded: chain D residue 1069 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 326 optimal weight: 0.1980 chunk 300 optimal weight: 0.5980 chunk 260 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 A 657 GLN ** A1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN ** B 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 ASN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4556 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= 0.196 Angle : 0.658 12.927 37708 Z= 0.321 Chirality : 0.042 0.287 4248 Planarity : 0.004 0.057 4632 Dihedral : 5.649 58.733 3836 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.52 % Allowed : 26.73 % Favored : 69.76 % Cbeta Deviations : 0.09 % 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: -0.83 (0.15), residues: 3232 helix: 0.34 (0.11), residues: 2124 sheet: -1.27 (0.45), residues: 144 loop : -2.37 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 984 HIS 0.003 0.001 HIS A 176 PHE 0.031 0.001 PHE D 969 TYR 0.017 0.001 TYR D 763 ARG 0.008 0.000 ARG B 655 ********************** 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 961 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 857 time to evaluate : 2.658 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: A 465 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.8881 (p) REVERT: A 469 LEU cc_start: 0.9509 (mp) cc_final: 0.8952 (mp) REVERT: A 498 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7461 (mmtp) REVERT: A 587 LYS cc_start: 0.8871 (ttmm) cc_final: 0.8534 (ttmm) REVERT: A 622 GLU cc_start: 0.7645 (tp30) cc_final: 0.7115 (tp30) REVERT: A 655 ARG cc_start: 0.8549 (mtp-110) cc_final: 0.8339 (ttm110) REVERT: A 657 GLN cc_start: 0.8512 (mt0) cc_final: 0.8266 (mt0) REVERT: A 669 LEU cc_start: 0.9301 (mt) cc_final: 0.9001 (mp) REVERT: A 682 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8535 (mmmm) REVERT: A 742 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7552 (tp) REVERT: A 825 ASP cc_start: 0.8424 (t0) cc_final: 0.8198 (t0) REVERT: A 856 ASP cc_start: 0.8552 (m-30) cc_final: 0.8344 (m-30) REVERT: A 899 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6341 (pp) REVERT: A 980 ASN cc_start: 0.8436 (t0) cc_final: 0.7656 (m110) REVERT: B 250 HIS cc_start: 0.8632 (m-70) cc_final: 0.8312 (m-70) REVERT: B 366 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8023 (mm-30) REVERT: B 469 LEU cc_start: 0.9495 (mp) cc_final: 0.8922 (mp) REVERT: B 498 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7681 (mmtt) REVERT: B 587 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8492 (ttmm) REVERT: B 612 TYR cc_start: 0.9154 (m-80) cc_final: 0.8685 (m-80) REVERT: B 613 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7223 (tp30) REVERT: B 672 GLN cc_start: 0.8545 (tp40) cc_final: 0.8222 (tp40) REVERT: B 682 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8619 (mmmm) REVERT: B 736 TYR cc_start: 0.9026 (t80) cc_final: 0.8433 (t80) REVERT: B 742 LEU cc_start: 0.7953 (tp) cc_final: 0.7533 (tp) REVERT: B 745 TYR cc_start: 0.7778 (t80) cc_final: 0.7559 (t80) REVERT: B 749 MET cc_start: 0.7613 (mmt) cc_final: 0.7232 (mmt) REVERT: B 858 PHE cc_start: 0.8296 (t80) cc_final: 0.7915 (t80) REVERT: B 861 LEU cc_start: 0.9388 (mt) cc_final: 0.9151 (mt) REVERT: B 899 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6326 (pp) REVERT: B 953 TYR cc_start: 0.7307 (t80) cc_final: 0.7067 (t80) REVERT: B 980 ASN cc_start: 0.8441 (t0) cc_final: 0.8069 (t0) REVERT: B 1070 HIS cc_start: 0.7918 (p-80) cc_final: 0.7377 (t70) REVERT: B 1081 ASP cc_start: 0.8861 (t70) cc_final: 0.8601 (t0) REVERT: C 250 HIS cc_start: 0.8676 (m-70) cc_final: 0.8394 (m-70) REVERT: C 312 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7893 (pttt) REVERT: C 469 LEU cc_start: 0.9441 (mp) cc_final: 0.8875 (mp) REVERT: C 498 LYS cc_start: 0.8131 (mmtp) cc_final: 0.7382 (mmtp) REVERT: C 613 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: C 622 GLU cc_start: 0.7541 (tp30) cc_final: 0.7106 (tp30) REVERT: C 627 ASP cc_start: 0.7166 (t70) cc_final: 0.6713 (t70) REVERT: C 656 ASP cc_start: 0.7914 (m-30) cc_final: 0.7357 (m-30) REVERT: C 672 GLN cc_start: 0.8551 (tp40) cc_final: 0.8291 (tp40) REVERT: C 682 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8627 (mmmm) REVERT: C 736 TYR cc_start: 0.9028 (t80) cc_final: 0.8347 (t80) REVERT: C 742 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7430 (tp) REVERT: C 745 TYR cc_start: 0.7725 (t80) cc_final: 0.7469 (t80) REVERT: C 749 MET cc_start: 0.7935 (mmp) cc_final: 0.7250 (mmt) REVERT: C 775 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6420 (tmt170) REVERT: C 953 TYR cc_start: 0.7328 (t80) cc_final: 0.7106 (t80) REVERT: C 969 PHE cc_start: 0.8102 (m-80) cc_final: 0.7848 (m-80) REVERT: C 980 ASN cc_start: 0.8546 (t0) cc_final: 0.8280 (t0) REVERT: C 1070 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.6669 (t-170) REVERT: D 454 PHE cc_start: 0.8671 (t80) cc_final: 0.8306 (t80) REVERT: D 469 LEU cc_start: 0.9545 (mp) cc_final: 0.9055 (mp) REVERT: D 474 ASN cc_start: 0.7847 (p0) cc_final: 0.7634 (p0) REVERT: D 498 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7822 (mmtt) REVERT: D 587 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8526 (ttmm) REVERT: D 592 MET cc_start: 0.8638 (mtp) cc_final: 0.8392 (ttm) REVERT: D 622 GLU cc_start: 0.7500 (tp30) cc_final: 0.7108 (tp30) REVERT: D 629 ASP cc_start: 0.8405 (m-30) cc_final: 0.8018 (m-30) REVERT: D 633 GLN cc_start: 0.8419 (mt0) cc_final: 0.7595 (mp10) REVERT: D 731 TRP cc_start: 0.8232 (t-100) cc_final: 0.7902 (t-100) REVERT: D 736 TYR cc_start: 0.8993 (t80) cc_final: 0.8379 (t80) REVERT: D 980 ASN cc_start: 0.8246 (t0) cc_final: 0.7485 (m110) REVERT: D 1049 MET cc_start: 0.8760 (ptm) cc_final: 0.8529 (ptm) REVERT: D 1081 ASP cc_start: 0.8963 (t70) cc_final: 0.8691 (t0) outliers start: 104 outliers final: 85 residues processed: 905 average time/residue: 0.3375 time to fit residues: 496.1490 Evaluate side-chains 929 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 833 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 688 MET Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 966 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 0.9980 chunk 277 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 260 optimal weight: 4.9990 chunk 109 optimal weight: 0.0370 chunk 267 optimal weight: 0.7980 chunk 32 optimal weight: 0.0570 chunk 48 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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** ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 GLN ** A1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 HIS ** 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 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 GLN ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.175328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145453 restraints weight = 42416.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149770 restraints weight = 24362.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152531 restraints weight = 17347.989| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 27856 Z= 0.314 Angle : 1.033 59.197 37708 Z= 0.589 Chirality : 0.068 2.006 4248 Planarity : 0.004 0.060 4632 Dihedral : 5.717 58.744 3836 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.12 % Favored : 92.76 % Rotamer: Outliers : 3.18 % Allowed : 27.37 % Favored : 69.45 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.82 (0.15), residues: 3232 helix: 0.35 (0.11), residues: 2124 sheet: -1.26 (0.45), residues: 144 loop : -2.38 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 984 HIS 0.003 0.001 HIS A 176 PHE 0.029 0.001 PHE D 969 TYR 0.017 0.001 TYR D 763 ARG 0.006 0.000 ARG C 655 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8177.14 seconds wall clock time: 146 minutes 3.98 seconds (8763.98 seconds total)