Starting phenix.real_space_refine on Sat Apr 13 13:44:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o77_0639/04_2024/6o77_0639.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o77_0639/04_2024/6o77_0639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o77_0639/04_2024/6o77_0639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o77_0639/04_2024/6o77_0639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o77_0639/04_2024/6o77_0639.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o77_0639/04_2024/6o77_0639.pdb" } resolution = 3.2 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 Ca 4 9.91 5 S 140 5.16 5 C 18884 2.51 5 N 4688 2.21 5 O 5168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 110": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A ARG 885": "NH1" <-> "NH2" Residue "A ARG 918": "NH1" <-> "NH2" Residue "A GLU 925": "OE1" <-> "OE2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "A GLU 1066": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 875": "NH1" <-> "NH2" Residue "B ARG 880": "NH1" <-> "NH2" Residue "B GLU 883": "OE1" <-> "OE2" Residue "B ARG 885": "NH1" <-> "NH2" Residue "B ARG 918": "NH1" <-> "NH2" Residue "B GLU 925": "OE1" <-> "OE2" Residue "B GLU 978": "OE1" <-> "OE2" Residue "B GLU 1051": "OE1" <-> "OE2" Residue "B GLU 1066": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C GLU 604": "OE1" <-> "OE2" Residue "C GLU 606": "OE1" <-> "OE2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C GLU 622": "OE1" <-> "OE2" Residue "C ARG 655": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 875": "NH1" <-> "NH2" Residue "C ARG 880": "NH1" <-> "NH2" Residue "C GLU 883": "OE1" <-> "OE2" Residue "C ARG 885": "NH1" <-> "NH2" Residue "C ARG 918": "NH1" <-> "NH2" Residue "C GLU 925": "OE1" <-> "OE2" Residue "C GLU 978": "OE1" <-> "OE2" Residue "C GLU 1051": "OE1" <-> "OE2" Residue "C GLU 1066": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D GLU 388": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D GLU 445": "OE1" <-> "OE2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D GLU 604": "OE1" <-> "OE2" Residue "D GLU 606": "OE1" <-> "OE2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "D GLU 622": "OE1" <-> "OE2" Residue "D ARG 655": "NH1" <-> "NH2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 875": "NH1" <-> "NH2" Residue "D ARG 880": "NH1" <-> "NH2" Residue "D GLU 883": "OE1" <-> "OE2" Residue "D ARG 885": "NH1" <-> "NH2" Residue "D ARG 918": "NH1" <-> "NH2" Residue "D GLU 925": "OE1" <-> "OE2" Residue "D GLU 978": "OE1" <-> "OE2" Residue "D GLU 1051": "OE1" <-> "OE2" Residue "D GLU 1066": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 28884 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 7115 Classifications: {'peptide': 872} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 849} Chain breaks: 11 Chain: "B" Number of atoms: 7115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 7115 Classifications: {'peptide': 872} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 849} Chain breaks: 11 Chain: "C" Number of atoms: 7115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 7115 Classifications: {'peptide': 872} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 849} Chain breaks: 11 Chain: "D" Number of atoms: 7115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 7115 Classifications: {'peptide': 872} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 849} Chain breaks: 11 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 15.14, per 1000 atoms: 0.52 Number of scatterers: 28884 At special positions: 0 Unit cell: (126.021, 126.021, 153.555, 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) Ca 4 19.99 S 140 16.00 O 5168 8.00 N 4688 7.00 C 18884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A 930 " distance=2.03 Simple disulfide: pdb=" SG CYS B 919 " - pdb=" SG CYS B 930 " distance=2.03 Simple disulfide: pdb=" SG CYS C 919 " - pdb=" SG CYS C 930 " distance=2.03 Simple disulfide: pdb=" SG CYS D 919 " - pdb=" SG CYS D 930 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.72 Conformation dependent library (CDL) restraints added in 4.9 seconds 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6632 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 8 sheets defined 65.8% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.579A pdb=" N HIS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.604A pdb=" N PHE A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 267 through 279 Processing helix chain 'A' and resid 300 through 313 removed outlier: 3.707A pdb=" N SER A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 removed outlier: 3.691A pdb=" N LYS A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 348 " --> pdb=" O CYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 376 removed outlier: 3.846A pdb=" N GLU A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 367 " --> pdb=" O GLU A 363 " (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 406 removed outlier: 3.995A pdb=" N PHE A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.735A pdb=" N GLN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.555A pdb=" N THR A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 459 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.622A pdb=" N ALA A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.970A pdb=" N LYS A 517 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 522 " --> pdb=" O MET A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 562 removed outlier: 3.640A pdb=" N ALA A 554 " --> pdb=" O HIS A 550 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 595 removed outlier: 3.639A pdb=" N ALA A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 654 removed outlier: 3.801A pdb=" N ALA A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.666A 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 675 Processing helix chain 'A' and resid 682 through 689 removed outlier: 3.921A pdb=" N ILE A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR A 723 " --> pdb=" O SER A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE A 735 " --> pdb=" O TRP A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 793 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR A 794 " --> pdb=" O ASN A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 831 removed outlier: 3.606A pdb=" N TYR A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 837 removed outlier: 4.156A pdb=" N HIS A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 851 removed outlier: 4.366A pdb=" N LYS A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 848 " --> pdb=" O GLY A 844 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 875 removed outlier: 3.535A pdb=" N ALA A 874 " --> pdb=" O ALA A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.561A pdb=" N ALA A 900 " --> pdb=" O GLU A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 959 removed outlier: 3.630A pdb=" N ASN A 958 " --> pdb=" O MET A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 976 removed outlier: 3.582A pdb=" N ALA A 967 " --> pdb=" O ASN A 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 972 " --> pdb=" O MET A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 994 removed outlier: 4.208A pdb=" N GLN A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A 990 " --> pdb=" O PHE A 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'A' and resid 1041 through 1061 removed outlier: 3.858A pdb=" N ALA A1061 " --> pdb=" O ILE A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP A1076 " --> pdb=" O PHE A1072 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A1077 " --> pdb=" O ARG A1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS A1078 " --> pdb=" O GLN A1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A1080 " --> pdb=" O ASP A1076 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A1093 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A1094 " --> pdb=" O SER A1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.580A pdb=" N HIS B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 167 removed outlier: 3.603A pdb=" N PHE B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.707A pdb=" N SER B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL B 334 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 348 removed outlier: 3.690A pdb=" N LYS B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 348 " --> pdb=" O CYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 376 removed outlier: 3.845A pdb=" N GLU B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B 367 " --> pdb=" O GLU B 363 " (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 406 removed outlier: 3.995A pdb=" N PHE B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.736A pdb=" N GLN B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA B 433 " --> pdb=" O GLN B 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 459 removed outlier: 3.554A pdb=" N THR B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 459 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 493 through 503 removed outlier: 3.621A pdb=" N ALA B 503 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 524 removed outlier: 3.970A pdb=" N LYS B 517 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 518 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 3.641A pdb=" N ALA B 554 " --> pdb=" O HIS B 550 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 562 " --> pdb=" O TRP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 595 removed outlier: 3.640A pdb=" N ALA B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 654 removed outlier: 3.801A pdb=" N ALA B 651 " --> pdb=" O CYS B 647 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 3.666A 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 675 Processing helix chain 'B' and resid 682 through 689 removed outlier: 3.920A pdb=" N ILE B 686 " --> pdb=" O LYS B 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR B 723 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE B 735 " --> pdb=" O TRP B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE B 760 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET B 792 " --> pdb=" O LEU B 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 793 " --> pdb=" O TRP B 789 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR B 794 " --> pdb=" O ASN B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 831 removed outlier: 3.606A pdb=" N TYR B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 837 removed outlier: 4.156A pdb=" N HIS B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 851 removed outlier: 4.367A pdb=" N LYS B 846 " --> pdb=" O ASN B 842 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 848 " --> pdb=" O GLY B 844 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 851 " --> pdb=" O ILE B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 875 removed outlier: 3.535A pdb=" N ALA B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 900 removed outlier: 3.562A pdb=" N ALA B 900 " --> pdb=" O GLU B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 959 removed outlier: 3.631A pdb=" N ASN B 958 " --> pdb=" O MET B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 976 removed outlier: 3.583A pdb=" N ALA B 967 " --> pdb=" O ASN B 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 972 " --> pdb=" O MET B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 994 removed outlier: 4.208A pdb=" N GLN B 982 " --> pdb=" O GLU B 978 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 989 " --> pdb=" O LYS B 985 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE B 990 " --> pdb=" O PHE B 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1008 Processing helix chain 'B' and resid 1041 through 1061 removed outlier: 3.858A pdb=" N ALA B1061 " --> pdb=" O ILE B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP B1076 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B1077 " --> pdb=" O ARG B1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS B1078 " --> pdb=" O GLN B1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B1080 " --> pdb=" O ASP B1076 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP B1081 " --> pdb=" O ALA B1077 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B1091 " --> pdb=" O LYS B1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B1093 " --> pdb=" O ILE B1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.579A pdb=" N HIS C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 167 removed outlier: 3.604A pdb=" N PHE C 156 " --> pdb=" O MET C 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 300 through 313 removed outlier: 3.707A pdb=" N SER C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL C 334 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 348 removed outlier: 3.690A pdb=" N LYS C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 348 " --> pdb=" O CYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 376 removed outlier: 3.846A pdb=" N GLU C 366 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C 367 " --> pdb=" O GLU C 363 " (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 406 removed outlier: 3.995A pdb=" N PHE C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.736A pdb=" N GLN C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA C 433 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 removed outlier: 3.554A pdb=" N THR C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 459 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 493 through 503 removed outlier: 3.622A pdb=" N ALA C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 524 removed outlier: 3.970A pdb=" N LYS C 517 " --> pdb=" O THR C 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET C 518 " --> pdb=" O PHE C 514 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 522 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 562 removed outlier: 3.640A pdb=" N ALA C 554 " --> pdb=" O HIS C 550 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN C 562 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL C 570 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 595 removed outlier: 3.638A pdb=" N ALA C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU C 583 " --> pdb=" O THR C 579 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 635 " --> pdb=" O ALA C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 654 removed outlier: 3.800A pdb=" N ALA C 651 " --> pdb=" O CYS C 647 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 3.666A 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 675 Processing helix chain 'C' and resid 682 through 689 removed outlier: 3.920A pdb=" N ILE C 686 " --> pdb=" O LYS C 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR C 723 " --> pdb=" O SER C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE C 735 " --> pdb=" O TRP C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE C 760 " --> pdb=" O THR C 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 787 Processing helix chain 'C' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET C 792 " --> pdb=" O LEU C 788 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP C 793 " --> pdb=" O TRP C 789 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR C 794 " --> pdb=" O ASN C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 831 removed outlier: 3.607A pdb=" N TYR C 816 " --> pdb=" O GLU C 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 837 removed outlier: 4.156A pdb=" N HIS C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 851 removed outlier: 4.367A pdb=" N LYS C 846 " --> pdb=" O ASN C 842 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 848 " --> pdb=" O GLY C 844 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 851 " --> pdb=" O ILE C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 875 removed outlier: 3.534A pdb=" N ALA C 874 " --> pdb=" O ALA C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 900 removed outlier: 3.561A pdb=" N ALA C 900 " --> pdb=" O GLU C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 959 removed outlier: 3.631A pdb=" N ASN C 958 " --> pdb=" O MET C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 976 removed outlier: 3.582A pdb=" N ALA C 967 " --> pdb=" O ASN C 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 972 " --> pdb=" O MET C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 994 removed outlier: 4.209A pdb=" N GLN C 982 " --> pdb=" O GLU C 978 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C 989 " --> pdb=" O LYS C 985 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 990 " --> pdb=" O PHE C 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'C' and resid 1041 through 1061 removed outlier: 3.857A pdb=" N ALA C1061 " --> pdb=" O ILE C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP C1076 " --> pdb=" O PHE C1072 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C1077 " --> pdb=" O ARG C1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS C1078 " --> pdb=" O GLN C1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C1079 " --> pdb=" O LEU C1075 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C1080 " --> pdb=" O ASP C1076 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP C1081 " --> pdb=" O ALA C1077 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C1091 " --> pdb=" O LYS C1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C1093 " --> pdb=" O ILE C1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS C1094 " --> pdb=" O SER C1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.579A pdb=" N HIS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 167 removed outlier: 3.604A pdb=" N PHE D 156 " --> pdb=" O MET D 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 Processing helix chain 'D' and resid 267 through 279 Processing helix chain 'D' and resid 300 through 313 removed outlier: 3.708A pdb=" N SER D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL D 334 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 348 removed outlier: 3.691A pdb=" N LYS D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 348 " --> pdb=" O CYS D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 376 removed outlier: 3.846A pdb=" N GLU D 366 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER D 367 " --> pdb=" O GLU D 363 " (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 406 removed outlier: 3.995A pdb=" N PHE D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.735A pdb=" N GLN D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA D 433 " --> pdb=" O GLN D 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 459 removed outlier: 3.554A pdb=" N THR D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 459 " --> pdb=" O THR D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 493 through 503 removed outlier: 3.622A pdb=" N ALA D 503 " --> pdb=" O ASN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 524 removed outlier: 3.969A pdb=" N LYS D 517 " --> pdb=" O THR D 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET D 518 " --> pdb=" O PHE D 514 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 3.640A pdb=" N ALA D 554 " --> pdb=" O HIS D 550 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN D 562 " --> pdb=" O TRP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 595 removed outlier: 3.638A pdb=" N ALA D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 614 " --> pdb=" O ASN D 610 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 635 " --> pdb=" O ALA D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 654 removed outlier: 3.800A pdb=" N ALA D 651 " --> pdb=" O CYS D 647 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 3.665A 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 675 Processing helix chain 'D' and resid 682 through 689 removed outlier: 3.920A pdb=" N ILE D 686 " --> pdb=" O LYS D 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR D 723 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE D 735 " --> pdb=" O TRP D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE D 760 " --> pdb=" O THR D 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 761 " --> pdb=" O ALA D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 787 Processing helix chain 'D' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP D 793 " --> pdb=" O TRP D 789 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR D 794 " --> pdb=" O ASN D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 831 removed outlier: 3.606A pdb=" N TYR D 816 " --> pdb=" O GLU D 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER D 817 " --> pdb=" O SER D 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 837 removed outlier: 4.157A pdb=" N HIS D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 851 removed outlier: 4.366A pdb=" N LYS D 846 " --> pdb=" O ASN D 842 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 848 " --> pdb=" O GLY D 844 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 851 " --> pdb=" O ILE D 847 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 875 removed outlier: 3.535A pdb=" N ALA D 874 " --> pdb=" O ALA D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 887 Processing helix chain 'D' and resid 894 through 900 removed outlier: 3.561A pdb=" N ALA D 900 " --> pdb=" O GLU D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 959 removed outlier: 3.631A pdb=" N ASN D 958 " --> pdb=" O MET D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 976 removed outlier: 3.583A pdb=" N ALA D 967 " --> pdb=" O ASN D 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 972 " --> pdb=" O MET D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 994 removed outlier: 4.209A pdb=" N GLN D 982 " --> pdb=" O GLU D 978 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE D 989 " --> pdb=" O LYS D 985 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE D 990 " --> pdb=" O PHE D 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1008 Processing helix chain 'D' and resid 1041 through 1061 removed outlier: 3.857A pdb=" N ALA D1061 " --> pdb=" O ILE D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP D1076 " --> pdb=" O PHE D1072 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D1077 " --> pdb=" O ARG D1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS D1078 " --> pdb=" O GLN D1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU D1079 " --> pdb=" O LEU D1075 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D1080 " --> pdb=" O ASP D1076 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP D1081 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D1091 " --> pdb=" O LYS D1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D1093 " --> pdb=" O ILE D1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS D1094 " --> pdb=" O SER D1090 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.792A pdb=" N LYS A 107 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU A 253 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 109 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA A 202 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 252 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY A 204 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU A 135 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N PHE A 295 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 137 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL A 319 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS A 294 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU A 321 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA A 296 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.792A pdb=" N LYS B 107 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU B 253 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 109 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA B 202 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU B 252 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY B 204 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 135 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE B 295 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE B 137 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL B 319 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS B 294 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU B 321 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA B 296 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 110 removed outlier: 6.791A pdb=" N LYS C 107 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU C 253 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE C 109 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA C 202 " --> pdb=" O HIS C 250 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU C 252 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY C 204 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 135 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE C 295 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE C 137 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL C 319 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS C 294 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU C 321 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA C 296 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 110 removed outlier: 6.793A pdb=" N LYS D 107 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU D 253 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE D 109 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA D 202 " --> pdb=" O HIS D 250 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU D 252 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY D 204 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU D 135 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE D 295 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE D 137 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL D 319 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS D 294 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU D 321 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA D 296 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 1340 hydrogen bonds defined for protein. 3984 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: 9.18 Time building geometry restraints manager: 11.53 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: 4644 1.31 - 1.43: 8156 1.43 - 1.56: 16412 1.56 - 1.69: 88 1.69 - 1.82: 252 Bond restraints: 29552 Sorted by residual: bond pdb=" CAI Y01 C1403 " pdb=" CAZ Y01 C1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 D1403 " pdb=" CAZ Y01 D1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 A1403 " pdb=" CAZ Y01 A1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 B1403 " pdb=" CAZ Y01 B1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 D1402 " pdb=" CAZ Y01 D1402 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.19e+02 ... (remaining 29547 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.88: 455 105.88 - 113.01: 15765 113.01 - 120.13: 11913 120.13 - 127.26: 11543 127.26 - 134.38: 356 Bond angle restraints: 40032 Sorted by residual: angle pdb=" C ASP D 907 " pdb=" N ASP D 908 " pdb=" CA ASP D 908 " ideal model delta sigma weight residual 121.83 112.81 9.02 1.48e+00 4.57e-01 3.71e+01 angle pdb=" C ASP A 907 " pdb=" N ASP A 908 " pdb=" CA ASP A 908 " ideal model delta sigma weight residual 121.83 112.82 9.01 1.48e+00 4.57e-01 3.70e+01 angle pdb=" C ASP C 907 " pdb=" N ASP C 908 " pdb=" CA ASP C 908 " ideal model delta sigma weight residual 121.83 112.82 9.01 1.48e+00 4.57e-01 3.70e+01 angle pdb=" C ASP B 907 " pdb=" N ASP B 908 " pdb=" CA ASP B 908 " ideal model delta sigma weight residual 121.83 112.83 9.00 1.48e+00 4.57e-01 3.70e+01 angle pdb=" N ASP A 907 " pdb=" CA ASP A 907 " pdb=" C ASP A 907 " ideal model delta sigma weight residual 111.33 118.07 -6.74 1.21e+00 6.83e-01 3.10e+01 ... (remaining 40027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15905 17.97 - 35.94: 1747 35.94 - 53.91: 264 53.91 - 71.88: 64 71.88 - 89.85: 28 Dihedral angle restraints: 18008 sinusoidal: 7804 harmonic: 10204 Sorted by residual: dihedral pdb=" CA GLN C 876 " pdb=" C GLN C 876 " pdb=" N GLY C 877 " pdb=" CA GLY C 877 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA GLN D 876 " pdb=" C GLN D 876 " pdb=" N GLY D 877 " pdb=" CA GLY D 877 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA GLN B 876 " pdb=" C GLN B 876 " pdb=" N GLY B 877 " pdb=" CA GLY B 877 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 18005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4285 0.114 - 0.228: 155 0.228 - 0.342: 24 0.342 - 0.456: 8 0.456 - 0.571: 12 Chirality restraints: 4484 Sorted by residual: chirality pdb=" CBI Y01 B1404 " pdb=" CAU Y01 B1404 " pdb=" CBE Y01 B1404 " pdb=" CBG Y01 B1404 " both_signs ideal model delta sigma weight residual False 2.94 2.37 0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" CBI Y01 D1404 " pdb=" CAU Y01 D1404 " pdb=" CBE Y01 D1404 " pdb=" CBG Y01 D1404 " both_signs ideal model delta sigma weight residual False 2.94 2.37 0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" CBI Y01 A1404 " pdb=" CAU Y01 A1404 " pdb=" CBE Y01 A1404 " pdb=" CBG Y01 A1404 " both_signs ideal model delta sigma weight residual False 2.94 2.37 0.57 2.00e-01 2.50e+01 8.08e+00 ... (remaining 4481 not shown) Planarity restraints: 4928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 905 " 0.108 5.00e-02 4.00e+02 1.64e-01 4.33e+01 pdb=" N PRO B 906 " -0.284 5.00e-02 4.00e+02 pdb=" CA PRO B 906 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO B 906 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 905 " -0.108 5.00e-02 4.00e+02 1.64e-01 4.33e+01 pdb=" N PRO C 906 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO C 906 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO C 906 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 905 " -0.108 5.00e-02 4.00e+02 1.64e-01 4.32e+01 pdb=" N PRO D 906 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO D 906 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO D 906 " -0.080 5.00e-02 4.00e+02 ... (remaining 4925 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 20 2.26 - 2.92: 11749 2.92 - 3.58: 40812 3.58 - 4.24: 69088 4.24 - 4.90: 113633 Nonbonded interactions: 235302 Sorted by model distance: nonbonded pdb=" CH2 TRP A 888 " pdb=" O SER A 926 " model vdw 1.604 3.340 nonbonded pdb=" CH2 TRP D 888 " pdb=" O SER D 926 " model vdw 1.604 3.340 nonbonded pdb=" CH2 TRP B 888 " pdb=" O SER B 926 " model vdw 1.604 3.340 nonbonded pdb=" CH2 TRP C 888 " pdb=" O SER C 926 " model vdw 1.604 3.340 nonbonded pdb=" CZ3 TRP D 888 " pdb=" O SER D 926 " model vdw 2.016 3.340 ... (remaining 235297 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.310 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 72.880 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.190 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.013 0.364 29552 Z= 0.755 Angle : 1.006 16.675 40032 Z= 0.517 Chirality : 0.063 0.571 4484 Planarity : 0.007 0.164 4928 Dihedral : 15.188 89.851 11364 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -5.77 (0.10), residues: 3392 helix: -4.01 (0.05), residues: 2156 sheet: -2.45 (0.33), residues: 208 loop : -3.09 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 516 HIS 0.009 0.002 HIS D 129 PHE 0.021 0.002 PHE B 806 TYR 0.016 0.002 TYR C 971 ARG 0.009 0.000 ARG C 655 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 953 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.8035 (ttt180) cc_final: 0.6297 (ptp-170) REVERT: A 149 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8587 (mtmt) REVERT: A 323 SER cc_start: 0.8415 (m) cc_final: 0.7928 (m) REVERT: A 592 MET cc_start: 0.8462 (mmm) cc_final: 0.8173 (mmp) REVERT: A 606 GLU cc_start: 0.8298 (pp20) cc_final: 0.7844 (pp20) REVERT: A 611 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7941 (mm-30) REVERT: A 649 GLU cc_start: 0.8034 (mp0) cc_final: 0.7663 (pm20) REVERT: A 672 GLN cc_start: 0.8006 (tt0) cc_final: 0.7767 (tt0) REVERT: A 674 TYR cc_start: 0.8269 (m-80) cc_final: 0.7897 (m-10) REVERT: A 775 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7543 (ttt180) REVERT: A 789 TRP cc_start: 0.8714 (m100) cc_final: 0.8308 (m100) REVERT: A 790 ASN cc_start: 0.9162 (m-40) cc_final: 0.8790 (t0) REVERT: A 798 PHE cc_start: 0.8640 (t80) cc_final: 0.8414 (t80) REVERT: A 825 ASP cc_start: 0.8431 (t0) cc_final: 0.8190 (t0) REVERT: A 841 ARG cc_start: 0.7177 (ttp80) cc_final: 0.6726 (ttp80) REVERT: A 887 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7366 (mt-10) REVERT: A 955 LEU cc_start: 0.9183 (tp) cc_final: 0.8924 (tp) REVERT: A 1056 LYS cc_start: 0.9017 (tmmt) cc_final: 0.8762 (ttpp) REVERT: B 110 ARG cc_start: 0.8070 (ttt180) cc_final: 0.6282 (ptp-170) REVERT: B 149 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8571 (mtmt) REVERT: B 592 MET cc_start: 0.8454 (mmm) cc_final: 0.8173 (mmp) REVERT: B 606 GLU cc_start: 0.8295 (pp20) cc_final: 0.7853 (pp20) REVERT: B 649 GLU cc_start: 0.8049 (mp0) cc_final: 0.7666 (pm20) REVERT: B 672 GLN cc_start: 0.8008 (tt0) cc_final: 0.7771 (tt0) REVERT: B 674 TYR cc_start: 0.8269 (m-80) cc_final: 0.7902 (m-10) REVERT: B 775 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7572 (ttt180) REVERT: B 789 TRP cc_start: 0.8720 (m100) cc_final: 0.8314 (m100) REVERT: B 790 ASN cc_start: 0.9164 (m-40) cc_final: 0.8792 (t0) REVERT: B 798 PHE cc_start: 0.8639 (t80) cc_final: 0.8390 (t80) REVERT: B 825 ASP cc_start: 0.8401 (t0) cc_final: 0.8152 (t0) REVERT: B 841 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6744 (ttp80) REVERT: B 887 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7351 (mt-10) REVERT: B 955 LEU cc_start: 0.9185 (tp) cc_final: 0.8938 (tp) REVERT: C 110 ARG cc_start: 0.8072 (ttt180) cc_final: 0.6281 (ptp-170) REVERT: C 149 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8571 (mtmt) REVERT: C 592 MET cc_start: 0.8454 (mmm) cc_final: 0.8174 (mmp) REVERT: C 606 GLU cc_start: 0.8300 (pp20) cc_final: 0.7856 (pp20) REVERT: C 649 GLU cc_start: 0.8046 (mp0) cc_final: 0.7661 (pm20) REVERT: C 672 GLN cc_start: 0.8006 (tt0) cc_final: 0.7771 (tt0) REVERT: C 674 TYR cc_start: 0.8270 (m-80) cc_final: 0.7899 (m-10) REVERT: C 775 ARG cc_start: 0.7777 (ttp80) cc_final: 0.7565 (ttt180) REVERT: C 789 TRP cc_start: 0.8721 (m100) cc_final: 0.8324 (m100) REVERT: C 790 ASN cc_start: 0.9164 (m-40) cc_final: 0.8786 (t0) REVERT: C 798 PHE cc_start: 0.8636 (t80) cc_final: 0.8389 (t80) REVERT: C 825 ASP cc_start: 0.8398 (t0) cc_final: 0.8147 (t0) REVERT: C 841 ARG cc_start: 0.7189 (ttp80) cc_final: 0.6744 (ttp80) REVERT: C 887 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7351 (mt-10) REVERT: C 955 LEU cc_start: 0.9185 (tp) cc_final: 0.8937 (tp) REVERT: D 110 ARG cc_start: 0.8069 (ttt180) cc_final: 0.6288 (ptp-170) REVERT: D 149 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8573 (mtmt) REVERT: D 592 MET cc_start: 0.8454 (mmm) cc_final: 0.8173 (mmp) REVERT: D 606 GLU cc_start: 0.8298 (pp20) cc_final: 0.7858 (pp20) REVERT: D 649 GLU cc_start: 0.8048 (mp0) cc_final: 0.7663 (pm20) REVERT: D 672 GLN cc_start: 0.8007 (tt0) cc_final: 0.7773 (tt0) REVERT: D 674 TYR cc_start: 0.8267 (m-80) cc_final: 0.7897 (m-10) REVERT: D 775 ARG cc_start: 0.7774 (ttp80) cc_final: 0.7564 (ttt180) REVERT: D 789 TRP cc_start: 0.8719 (m100) cc_final: 0.8324 (m100) REVERT: D 790 ASN cc_start: 0.9163 (m-40) cc_final: 0.8789 (t0) REVERT: D 798 PHE cc_start: 0.8637 (t80) cc_final: 0.8389 (t80) REVERT: D 825 ASP cc_start: 0.8401 (t0) cc_final: 0.8148 (t0) REVERT: D 841 ARG cc_start: 0.7190 (ttp80) cc_final: 0.6747 (ttp80) REVERT: D 887 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7391 (mt-10) REVERT: D 955 LEU cc_start: 0.9185 (tp) cc_final: 0.8935 (tp) outliers start: 0 outliers final: 0 residues processed: 953 average time/residue: 0.4641 time to fit residues: 673.3322 Evaluate side-chains 771 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 771 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 0.2980 chunk 263 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 177 optimal weight: 0.2980 chunk 140 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 316 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 213 ASN A 248 HIS A 440 ASN A 499 ASN A 662 GLN A 666 GLN A 683 ASN A 882 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 GLN B 145 ASN B 213 ASN B 248 HIS B 440 ASN B 499 ASN B 662 GLN B 666 GLN B 683 ASN B 882 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 GLN C 145 ASN C 213 ASN C 248 HIS C 440 ASN C 499 ASN C 662 GLN C 666 GLN C 683 ASN C 882 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 GLN D 145 ASN D 213 ASN D 248 HIS D 440 ASN D 499 ASN D 662 GLN D 666 GLN D 683 ASN D 882 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 29552 Z= 0.204 Angle : 0.659 11.481 40032 Z= 0.341 Chirality : 0.042 0.206 4484 Planarity : 0.006 0.147 4928 Dihedral : 7.618 53.314 4588 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.31 % Favored : 93.57 % Rotamer: Outliers : 1.86 % Allowed : 14.20 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -3.35 (0.12), residues: 3392 helix: -1.78 (0.09), residues: 2216 sheet: -1.97 (0.36), residues: 196 loop : -2.90 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 444 HIS 0.004 0.001 HIS A 129 PHE 0.025 0.001 PHE D 921 TYR 0.018 0.001 TYR C 905 ARG 0.005 0.000 ARG C 875 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 802 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.8062 (ttt180) cc_final: 0.6276 (ptp-170) REVERT: A 323 SER cc_start: 0.8227 (m) cc_final: 0.7965 (m) REVERT: A 435 ASP cc_start: 0.8193 (m-30) cc_final: 0.7758 (m-30) REVERT: A 592 MET cc_start: 0.8419 (mmm) cc_final: 0.8036 (mmp) REVERT: A 611 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 649 GLU cc_start: 0.8020 (mp0) cc_final: 0.7598 (pm20) REVERT: A 672 GLN cc_start: 0.8017 (tt0) cc_final: 0.7737 (tt0) REVERT: A 674 TYR cc_start: 0.8282 (m-80) cc_final: 0.8008 (m-10) REVERT: A 688 MET cc_start: 0.7800 (mtt) cc_final: 0.6542 (tmm) REVERT: A 775 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7455 (ttt180) REVERT: A 785 PHE cc_start: 0.8379 (m-10) cc_final: 0.8105 (m-80) REVERT: A 789 TRP cc_start: 0.8702 (m100) cc_final: 0.8416 (m100) REVERT: A 790 ASN cc_start: 0.9146 (m-40) cc_final: 0.8755 (t0) REVERT: A 798 PHE cc_start: 0.8609 (t80) cc_final: 0.8397 (t80) REVERT: A 825 ASP cc_start: 0.8287 (t0) cc_final: 0.8072 (t0) REVERT: A 832 ARG cc_start: 0.8438 (tpp80) cc_final: 0.8173 (mtp85) REVERT: A 841 ARG cc_start: 0.7231 (ttp80) cc_final: 0.6828 (ttp80) REVERT: A 853 MET cc_start: 0.8302 (mmt) cc_final: 0.8018 (mmt) REVERT: B 110 ARG cc_start: 0.8073 (ttt180) cc_final: 0.6340 (ptp-170) REVERT: B 553 GLN cc_start: 0.7061 (mp10) cc_final: 0.6274 (mp10) REVERT: B 592 MET cc_start: 0.8418 (mmm) cc_final: 0.8033 (mmp) REVERT: B 607 GLU cc_start: 0.8549 (tp30) cc_final: 0.8075 (tp30) REVERT: B 649 GLU cc_start: 0.8007 (mp0) cc_final: 0.7576 (pm20) REVERT: B 672 GLN cc_start: 0.8013 (tt0) cc_final: 0.7731 (tt0) REVERT: B 674 TYR cc_start: 0.8286 (m-80) cc_final: 0.8007 (m-10) REVERT: B 688 MET cc_start: 0.7813 (mtt) cc_final: 0.6552 (tmm) REVERT: B 775 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7452 (ttt180) REVERT: B 789 TRP cc_start: 0.8705 (m100) cc_final: 0.8416 (m100) REVERT: B 790 ASN cc_start: 0.9165 (m-40) cc_final: 0.8736 (t0) REVERT: B 798 PHE cc_start: 0.8606 (t80) cc_final: 0.8402 (t80) REVERT: B 825 ASP cc_start: 0.8283 (t0) cc_final: 0.8080 (t0) REVERT: B 841 ARG cc_start: 0.7280 (ttp80) cc_final: 0.6896 (ttp80) REVERT: B 853 MET cc_start: 0.8307 (mmt) cc_final: 0.8015 (mmt) REVERT: C 110 ARG cc_start: 0.8073 (ttt180) cc_final: 0.6342 (ptp-170) REVERT: C 553 GLN cc_start: 0.7054 (mp10) cc_final: 0.6272 (mp10) REVERT: C 592 MET cc_start: 0.8419 (mmm) cc_final: 0.8031 (mmp) REVERT: C 607 GLU cc_start: 0.8548 (tp30) cc_final: 0.8074 (tp30) REVERT: C 649 GLU cc_start: 0.8006 (mp0) cc_final: 0.7571 (pm20) REVERT: C 672 GLN cc_start: 0.8014 (tt0) cc_final: 0.7731 (tt0) REVERT: C 674 TYR cc_start: 0.8285 (m-80) cc_final: 0.8003 (m-10) REVERT: C 688 MET cc_start: 0.7813 (mtt) cc_final: 0.6554 (tmm) REVERT: C 775 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7453 (ttt180) REVERT: C 785 PHE cc_start: 0.8384 (m-10) cc_final: 0.7789 (m-80) REVERT: C 789 TRP cc_start: 0.8706 (m100) cc_final: 0.8414 (m100) REVERT: C 790 ASN cc_start: 0.9148 (m-40) cc_final: 0.8746 (t0) REVERT: C 798 PHE cc_start: 0.8602 (t80) cc_final: 0.8397 (t80) REVERT: C 825 ASP cc_start: 0.8280 (t0) cc_final: 0.8079 (t0) REVERT: C 841 ARG cc_start: 0.7241 (ttp80) cc_final: 0.6841 (ttp80) REVERT: C 853 MET cc_start: 0.8309 (mmt) cc_final: 0.8015 (mmt) REVERT: C 1068 MET cc_start: 0.4358 (ttt) cc_final: 0.4150 (pmm) REVERT: D 110 ARG cc_start: 0.8073 (ttt180) cc_final: 0.6339 (ptp-170) REVERT: D 553 GLN cc_start: 0.7057 (mp10) cc_final: 0.6272 (mp10) REVERT: D 592 MET cc_start: 0.8417 (mmm) cc_final: 0.8033 (mmp) REVERT: D 607 GLU cc_start: 0.8551 (tp30) cc_final: 0.8074 (tp30) REVERT: D 649 GLU cc_start: 0.8029 (mp0) cc_final: 0.7597 (pm20) REVERT: D 672 GLN cc_start: 0.8014 (tt0) cc_final: 0.7733 (tt0) REVERT: D 674 TYR cc_start: 0.8284 (m-80) cc_final: 0.8003 (m-10) REVERT: D 688 MET cc_start: 0.7812 (mtt) cc_final: 0.6552 (tmm) REVERT: D 775 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7454 (ttt180) REVERT: D 789 TRP cc_start: 0.8700 (m100) cc_final: 0.8411 (m100) REVERT: D 790 ASN cc_start: 0.9150 (m-40) cc_final: 0.8746 (t0) REVERT: D 798 PHE cc_start: 0.8602 (t80) cc_final: 0.8398 (t80) REVERT: D 841 ARG cc_start: 0.7279 (ttp80) cc_final: 0.6898 (ttp80) REVERT: D 853 MET cc_start: 0.8306 (mmt) cc_final: 0.8015 (mmt) outliers start: 58 outliers final: 36 residues processed: 821 average time/residue: 0.4278 time to fit residues: 548.6239 Evaluate side-chains 755 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 719 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 793 ASP Chi-restraints excluded: chain D residue 888 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 263 optimal weight: 0.5980 chunk 215 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 316 optimal weight: 0.7980 chunk 342 optimal weight: 6.9990 chunk 281 optimal weight: 0.0030 chunk 313 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 29552 Z= 0.172 Angle : 0.578 11.109 40032 Z= 0.298 Chirality : 0.041 0.190 4484 Planarity : 0.005 0.137 4928 Dihedral : 6.919 49.515 4588 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.07 % Favored : 93.81 % Rotamer: Outliers : 2.86 % Allowed : 15.91 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -2.14 (0.14), residues: 3392 helix: -0.68 (0.11), residues: 2216 sheet: -1.69 (0.38), residues: 196 loop : -2.84 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 444 HIS 0.004 0.001 HIS A 129 PHE 0.013 0.001 PHE D 921 TYR 0.012 0.001 TYR B 905 ARG 0.005 0.000 ARG A 875 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 812 time to evaluate : 3.225 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: A 110 ARG cc_start: 0.8022 (ttt180) cc_final: 0.6296 (ptp-170) REVERT: A 323 SER cc_start: 0.8183 (m) cc_final: 0.7894 (m) REVERT: A 435 ASP cc_start: 0.8237 (m-30) cc_final: 0.7851 (m-30) REVERT: A 592 MET cc_start: 0.8393 (mmm) cc_final: 0.8010 (mmp) REVERT: A 611 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 674 TYR cc_start: 0.8273 (m-80) cc_final: 0.7980 (m-80) REVERT: A 688 MET cc_start: 0.7731 (mtt) cc_final: 0.6405 (tmm) REVERT: A 775 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7412 (ttt180) REVERT: A 785 PHE cc_start: 0.8319 (m-10) cc_final: 0.8046 (m-10) REVERT: A 789 TRP cc_start: 0.8707 (m100) cc_final: 0.8465 (m100) REVERT: A 790 ASN cc_start: 0.9089 (m-40) cc_final: 0.8789 (t0) REVERT: A 798 PHE cc_start: 0.8522 (t80) cc_final: 0.8288 (t80) REVERT: A 832 ARG cc_start: 0.8427 (tpp80) cc_final: 0.8114 (mtp85) REVERT: A 841 ARG cc_start: 0.7162 (ttp80) cc_final: 0.6823 (ttp80) REVERT: B 110 ARG cc_start: 0.8055 (ttt180) cc_final: 0.6348 (ptp-170) REVERT: B 435 ASP cc_start: 0.8236 (m-30) cc_final: 0.7856 (m-30) REVERT: B 592 MET cc_start: 0.8390 (mmm) cc_final: 0.8020 (mmp) REVERT: B 607 GLU cc_start: 0.8534 (tp30) cc_final: 0.8105 (tp30) REVERT: B 649 GLU cc_start: 0.8053 (mp0) cc_final: 0.7564 (mp0) REVERT: B 674 TYR cc_start: 0.8276 (m-80) cc_final: 0.7977 (m-80) REVERT: B 688 MET cc_start: 0.7664 (mtt) cc_final: 0.6373 (tmm) REVERT: B 775 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7411 (ttt180) REVERT: B 784 TYR cc_start: 0.7574 (t80) cc_final: 0.7058 (t80) REVERT: B 789 TRP cc_start: 0.8714 (m100) cc_final: 0.8454 (m100) REVERT: B 790 ASN cc_start: 0.9098 (m-40) cc_final: 0.8743 (t0) REVERT: B 798 PHE cc_start: 0.8499 (t80) cc_final: 0.8248 (t80) REVERT: B 832 ARG cc_start: 0.8352 (tpp80) cc_final: 0.8055 (mtp85) REVERT: B 841 ARG cc_start: 0.7247 (ttp80) cc_final: 0.6934 (ttp80) REVERT: B 977 GLN cc_start: 0.8209 (tp40) cc_final: 0.7877 (tp40) REVERT: B 1068 MET cc_start: 0.4539 (pmm) cc_final: 0.3999 (mtt) REVERT: C 110 ARG cc_start: 0.8056 (ttt180) cc_final: 0.6348 (ptp-170) REVERT: C 435 ASP cc_start: 0.8266 (m-30) cc_final: 0.7894 (m-30) REVERT: C 592 MET cc_start: 0.8389 (mmm) cc_final: 0.8018 (mmp) REVERT: C 607 GLU cc_start: 0.8533 (tp30) cc_final: 0.8106 (tp30) REVERT: C 674 TYR cc_start: 0.8276 (m-80) cc_final: 0.7984 (m-80) REVERT: C 688 MET cc_start: 0.7725 (mtt) cc_final: 0.6405 (tmm) REVERT: C 775 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7418 (ttt180) REVERT: C 784 TYR cc_start: 0.7595 (t80) cc_final: 0.7073 (t80) REVERT: C 789 TRP cc_start: 0.8730 (m100) cc_final: 0.8500 (m100) REVERT: C 790 ASN cc_start: 0.9084 (m-40) cc_final: 0.8736 (t0) REVERT: C 798 PHE cc_start: 0.8501 (t80) cc_final: 0.8254 (t80) REVERT: C 841 ARG cc_start: 0.7209 (ttp80) cc_final: 0.6873 (ttp80) REVERT: C 853 MET cc_start: 0.8276 (mmt) cc_final: 0.8075 (mmt) REVERT: C 977 GLN cc_start: 0.8213 (tp40) cc_final: 0.7882 (tp40) REVERT: C 1068 MET cc_start: 0.4519 (ttt) cc_final: 0.3617 (pmm) REVERT: D 110 ARG cc_start: 0.8056 (ttt180) cc_final: 0.6348 (ptp-170) REVERT: D 435 ASP cc_start: 0.8261 (m-30) cc_final: 0.7894 (m-30) REVERT: D 592 MET cc_start: 0.8389 (mmm) cc_final: 0.8021 (mmp) REVERT: D 607 GLU cc_start: 0.8534 (tp30) cc_final: 0.8104 (tp30) REVERT: D 649 GLU cc_start: 0.8051 (mp0) cc_final: 0.7559 (mp0) REVERT: D 674 TYR cc_start: 0.8277 (m-80) cc_final: 0.7983 (m-80) REVERT: D 688 MET cc_start: 0.7664 (mtt) cc_final: 0.6372 (tmm) REVERT: D 775 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7413 (ttt180) REVERT: D 784 TYR cc_start: 0.7588 (t80) cc_final: 0.7058 (t80) REVERT: D 789 TRP cc_start: 0.8708 (m100) cc_final: 0.8478 (m100) REVERT: D 790 ASN cc_start: 0.9087 (m-40) cc_final: 0.8731 (t0) REVERT: D 798 PHE cc_start: 0.8500 (t80) cc_final: 0.8255 (t80) REVERT: D 841 ARG cc_start: 0.7252 (ttp80) cc_final: 0.6935 (ttp80) REVERT: D 853 MET cc_start: 0.8274 (mmt) cc_final: 0.8073 (mmt) REVERT: D 977 GLN cc_start: 0.8214 (tp40) cc_final: 0.7879 (tp40) outliers start: 89 outliers final: 53 residues processed: 849 average time/residue: 0.4206 time to fit residues: 564.0744 Evaluate side-chains 786 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 733 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 905 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 793 ASP Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 905 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 4.9990 chunk 238 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 chunk 317 optimal weight: 0.0870 chunk 336 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 301 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN B 732 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN D 732 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 29552 Z= 0.187 Angle : 0.572 10.952 40032 Z= 0.295 Chirality : 0.041 0.190 4484 Planarity : 0.005 0.132 4928 Dihedral : 6.637 49.750 4588 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.28 % Favored : 93.60 % Rotamer: Outliers : 2.92 % Allowed : 18.09 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.57 (0.14), residues: 3392 helix: -0.20 (0.11), residues: 2208 sheet: -1.55 (0.38), residues: 196 loop : -2.73 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 444 HIS 0.004 0.001 HIS A 129 PHE 0.016 0.001 PHE C 921 TYR 0.013 0.001 TYR A 784 ARG 0.004 0.000 ARG C 875 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 778 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.8022 (ttt180) cc_final: 0.6285 (ptp-170) REVERT: A 306 SER cc_start: 0.9112 (t) cc_final: 0.8521 (p) REVERT: A 323 SER cc_start: 0.8184 (m) cc_final: 0.7901 (m) REVERT: A 435 ASP cc_start: 0.8244 (m-30) cc_final: 0.7901 (m-30) REVERT: A 592 MET cc_start: 0.8412 (mmm) cc_final: 0.8173 (mmp) REVERT: A 611 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7796 (mm-30) REVERT: A 628 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7788 (mt-10) REVERT: A 674 TYR cc_start: 0.8276 (m-80) cc_final: 0.7964 (m-80) REVERT: A 688 MET cc_start: 0.7683 (mtt) cc_final: 0.6380 (tmm) REVERT: A 789 TRP cc_start: 0.8705 (m100) cc_final: 0.8439 (m100) REVERT: A 790 ASN cc_start: 0.9132 (m-40) cc_final: 0.8770 (t0) REVERT: A 798 PHE cc_start: 0.8452 (t80) cc_final: 0.8232 (t80) REVERT: A 841 ARG cc_start: 0.7221 (ttp80) cc_final: 0.6911 (ttp80) REVERT: A 1049 MET cc_start: 0.7439 (ptm) cc_final: 0.7137 (ttp) REVERT: B 110 ARG cc_start: 0.8057 (ttt180) cc_final: 0.6288 (ptp-170) REVERT: B 306 SER cc_start: 0.9120 (t) cc_final: 0.8524 (p) REVERT: B 592 MET cc_start: 0.8398 (mmm) cc_final: 0.8156 (mmp) REVERT: B 607 GLU cc_start: 0.8531 (tp30) cc_final: 0.8158 (tp30) REVERT: B 628 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7795 (mt-10) REVERT: B 649 GLU cc_start: 0.8012 (mp0) cc_final: 0.7521 (mp0) REVERT: B 674 TYR cc_start: 0.8276 (m-80) cc_final: 0.8014 (m-80) REVERT: B 688 MET cc_start: 0.7701 (mtt) cc_final: 0.6442 (tmm) REVERT: B 784 TYR cc_start: 0.7827 (t80) cc_final: 0.7548 (t80) REVERT: B 789 TRP cc_start: 0.8695 (m100) cc_final: 0.8439 (m100) REVERT: B 790 ASN cc_start: 0.9080 (m-40) cc_final: 0.8827 (t0) REVERT: B 798 PHE cc_start: 0.8453 (t80) cc_final: 0.8235 (t80) REVERT: B 832 ARG cc_start: 0.8379 (tpp80) cc_final: 0.8038 (mtp85) REVERT: B 841 ARG cc_start: 0.7291 (ttp80) cc_final: 0.7004 (ttp80) REVERT: C 110 ARG cc_start: 0.8056 (ttt180) cc_final: 0.6290 (ptp-170) REVERT: C 306 SER cc_start: 0.9120 (t) cc_final: 0.8524 (p) REVERT: C 435 ASP cc_start: 0.8253 (m-30) cc_final: 0.7900 (m-30) REVERT: C 592 MET cc_start: 0.8398 (mmm) cc_final: 0.8156 (mmp) REVERT: C 607 GLU cc_start: 0.8529 (tp30) cc_final: 0.8158 (tp30) REVERT: C 628 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7788 (mt-10) REVERT: C 674 TYR cc_start: 0.8277 (m-80) cc_final: 0.8013 (m-80) REVERT: C 688 MET cc_start: 0.7677 (mtt) cc_final: 0.6381 (tmm) REVERT: C 784 TYR cc_start: 0.7849 (t80) cc_final: 0.7472 (t80) REVERT: C 789 TRP cc_start: 0.8711 (m100) cc_final: 0.8490 (m100) REVERT: C 790 ASN cc_start: 0.9108 (m-40) cc_final: 0.8832 (t0) REVERT: C 798 PHE cc_start: 0.8455 (t80) cc_final: 0.8239 (t80) REVERT: C 841 ARG cc_start: 0.7224 (ttp80) cc_final: 0.6909 (ttp80) REVERT: C 1049 MET cc_start: 0.7440 (ptm) cc_final: 0.7145 (ttp) REVERT: C 1068 MET cc_start: 0.4479 (ttt) cc_final: 0.3564 (pmm) REVERT: D 110 ARG cc_start: 0.8058 (ttt180) cc_final: 0.6288 (ptp-170) REVERT: D 306 SER cc_start: 0.9120 (t) cc_final: 0.8523 (p) REVERT: D 435 ASP cc_start: 0.8250 (m-30) cc_final: 0.7903 (m-30) REVERT: D 592 MET cc_start: 0.8398 (mmm) cc_final: 0.8157 (mmp) REVERT: D 607 GLU cc_start: 0.8530 (tp30) cc_final: 0.8157 (tp30) REVERT: D 628 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7790 (mt-10) REVERT: D 649 GLU cc_start: 0.8012 (mp0) cc_final: 0.7524 (mp0) REVERT: D 674 TYR cc_start: 0.8277 (m-80) cc_final: 0.8015 (m-80) REVERT: D 688 MET cc_start: 0.7702 (mtt) cc_final: 0.6441 (tmm) REVERT: D 784 TYR cc_start: 0.7844 (t80) cc_final: 0.7550 (t80) REVERT: D 789 TRP cc_start: 0.8690 (m100) cc_final: 0.8463 (m100) REVERT: D 790 ASN cc_start: 0.9106 (m-40) cc_final: 0.8838 (t0) REVERT: D 798 PHE cc_start: 0.8458 (t80) cc_final: 0.8240 (t80) REVERT: D 841 ARG cc_start: 0.7295 (ttp80) cc_final: 0.7002 (ttp80) REVERT: D 1049 MET cc_start: 0.7441 (ptm) cc_final: 0.7149 (ttp) outliers start: 91 outliers final: 63 residues processed: 812 average time/residue: 0.4099 time to fit residues: 532.8546 Evaluate side-chains 788 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 725 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 732 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 732 ASN Chi-restraints excluded: chain D residue 778 TYR Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 793 ASP Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 896 GLU Chi-restraints excluded: chain D residue 975 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 250 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 GLN A 732 ASN A 835 HIS ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 GLN B 835 HIS ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 GLN C 732 ASN C 835 HIS ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 GLN D 835 HIS ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 29552 Z= 0.368 Angle : 0.663 11.070 40032 Z= 0.340 Chirality : 0.045 0.188 4484 Planarity : 0.005 0.123 4928 Dihedral : 6.728 51.859 4588 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.28 % Favored : 91.60 % Rotamer: Outliers : 4.05 % Allowed : 18.16 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.38 (0.15), residues: 3392 helix: -0.06 (0.11), residues: 2220 sheet: -1.62 (0.37), residues: 196 loop : -2.63 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 731 HIS 0.006 0.001 HIS B 129 PHE 0.015 0.002 PHE D 620 TYR 0.013 0.001 TYR A 971 ARG 0.003 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 764 time to evaluate : 3.516 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 110 ARG cc_start: 0.8042 (ttt180) cc_final: 0.6343 (ptp90) REVERT: A 323 SER cc_start: 0.8325 (m) cc_final: 0.8061 (m) REVERT: A 486 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7843 (mm-30) REVERT: A 553 GLN cc_start: 0.7155 (mp10) cc_final: 0.6274 (mp10) REVERT: A 592 MET cc_start: 0.8350 (mmm) cc_final: 0.8146 (mmp) REVERT: A 611 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7759 (mm-30) REVERT: A 674 TYR cc_start: 0.8321 (m-80) cc_final: 0.7969 (m-10) REVERT: A 688 MET cc_start: 0.7760 (mtt) cc_final: 0.6449 (tmm) REVERT: A 785 PHE cc_start: 0.8390 (m-80) cc_final: 0.8043 (m-10) REVERT: A 790 ASN cc_start: 0.9145 (m-40) cc_final: 0.8735 (t0) REVERT: A 798 PHE cc_start: 0.8547 (t80) cc_final: 0.8325 (t80) REVERT: A 841 ARG cc_start: 0.7364 (ttp80) cc_final: 0.7038 (ttp80) REVERT: B 110 ARG cc_start: 0.8086 (ttt180) cc_final: 0.6336 (ptp90) REVERT: B 181 LYS cc_start: 0.9091 (tttt) cc_final: 0.8828 (ttpt) REVERT: B 486 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 592 MET cc_start: 0.8355 (mmm) cc_final: 0.8154 (mmp) REVERT: B 606 GLU cc_start: 0.8325 (pp20) cc_final: 0.7857 (pp20) REVERT: B 649 GLU cc_start: 0.8021 (mp0) cc_final: 0.7456 (mp0) REVERT: B 674 TYR cc_start: 0.8304 (m-80) cc_final: 0.7948 (m-10) REVERT: B 688 MET cc_start: 0.7768 (mtt) cc_final: 0.6444 (tmm) REVERT: B 784 TYR cc_start: 0.8124 (t80) cc_final: 0.7883 (t80) REVERT: B 790 ASN cc_start: 0.9123 (m-40) cc_final: 0.8784 (t0) REVERT: B 798 PHE cc_start: 0.8519 (t80) cc_final: 0.8269 (t80) REVERT: B 808 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 841 ARG cc_start: 0.7436 (ttp80) cc_final: 0.7132 (ttp80) REVERT: B 905 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6714 (t80) REVERT: C 110 ARG cc_start: 0.8086 (ttt180) cc_final: 0.6337 (ptp90) REVERT: C 553 GLN cc_start: 0.7154 (mp10) cc_final: 0.6279 (mp10) REVERT: C 592 MET cc_start: 0.8358 (mmm) cc_final: 0.8154 (mmp) REVERT: C 606 GLU cc_start: 0.8324 (pp20) cc_final: 0.7852 (pp20) REVERT: C 611 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7781 (mm-30) REVERT: C 674 TYR cc_start: 0.8320 (m-80) cc_final: 0.7965 (m-10) REVERT: C 688 MET cc_start: 0.7762 (mtt) cc_final: 0.6434 (tmm) REVERT: C 784 TYR cc_start: 0.8082 (t80) cc_final: 0.7831 (t80) REVERT: C 790 ASN cc_start: 0.9150 (m-40) cc_final: 0.8798 (t0) REVERT: C 798 PHE cc_start: 0.8526 (t80) cc_final: 0.8275 (t80) REVERT: C 808 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8256 (mm) REVERT: C 841 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7054 (ttp80) REVERT: C 905 TYR cc_start: 0.7586 (p90) cc_final: 0.6721 (t80) REVERT: C 1068 MET cc_start: 0.4574 (ttt) cc_final: 0.3900 (pmm) REVERT: D 110 ARG cc_start: 0.8086 (ttt180) cc_final: 0.6336 (ptp90) REVERT: D 486 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7842 (mm-30) REVERT: D 592 MET cc_start: 0.8356 (mmm) cc_final: 0.8155 (mmp) REVERT: D 606 GLU cc_start: 0.8327 (pp20) cc_final: 0.7860 (pp20) REVERT: D 649 GLU cc_start: 0.8017 (mp0) cc_final: 0.7455 (mp0) REVERT: D 674 TYR cc_start: 0.8307 (m-80) cc_final: 0.8011 (m-10) REVERT: D 688 MET cc_start: 0.7767 (mtt) cc_final: 0.6442 (tmm) REVERT: D 784 TYR cc_start: 0.8144 (t80) cc_final: 0.7905 (t80) REVERT: D 790 ASN cc_start: 0.9160 (m-40) cc_final: 0.8819 (t0) REVERT: D 798 PHE cc_start: 0.8530 (t80) cc_final: 0.8287 (t80) REVERT: D 808 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8273 (mm) REVERT: D 841 ARG cc_start: 0.7435 (ttp80) cc_final: 0.7134 (ttp80) REVERT: D 905 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6719 (t80) outliers start: 126 outliers final: 106 residues processed: 813 average time/residue: 0.4046 time to fit residues: 522.0140 Evaluate side-chains 835 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 724 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 417 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 417 TRP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 417 TRP Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 732 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 945 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 793 ASP Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 896 GLU Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 945 ILE Chi-restraints excluded: chain D residue 975 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 0.9990 chunk 302 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 336 optimal weight: 10.0000 chunk 279 optimal weight: 0.0970 chunk 155 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS A 646 ASN A 662 GLN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN B 127 HIS B 662 GLN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN C 429 GLN C 646 ASN C 662 GLN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 ASN D 127 HIS D 429 GLN D 662 GLN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 29552 Z= 0.183 Angle : 0.588 10.276 40032 Z= 0.302 Chirality : 0.042 0.207 4484 Planarity : 0.005 0.117 4928 Dihedral : 6.462 51.831 4588 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.13 % Favored : 92.75 % Rotamer: Outliers : 3.37 % Allowed : 19.38 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.03 (0.15), residues: 3392 helix: 0.22 (0.11), residues: 2204 sheet: -1.40 (0.38), residues: 196 loop : -2.49 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 516 HIS 0.003 0.001 HIS C 129 PHE 0.015 0.001 PHE C 921 TYR 0.014 0.001 TYR C 905 ARG 0.004 0.000 ARG D 832 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 786 time to evaluate : 3.811 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: A 110 ARG cc_start: 0.8009 (ttt180) cc_final: 0.6321 (ptp90) REVERT: A 323 SER cc_start: 0.8315 (m) cc_final: 0.8025 (m) REVERT: A 435 ASP cc_start: 0.8222 (m-30) cc_final: 0.7850 (m-30) REVERT: A 486 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7649 (mm-30) REVERT: A 553 GLN cc_start: 0.7061 (mp10) cc_final: 0.6149 (mp10) REVERT: A 606 GLU cc_start: 0.8292 (pp20) cc_final: 0.7821 (pp20) REVERT: A 613 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 628 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7830 (mt-10) REVERT: A 674 TYR cc_start: 0.8293 (m-80) cc_final: 0.7966 (m-80) REVERT: A 688 MET cc_start: 0.7705 (mtt) cc_final: 0.6457 (tmm) REVERT: A 785 PHE cc_start: 0.8367 (m-80) cc_final: 0.7990 (m-10) REVERT: A 790 ASN cc_start: 0.9127 (m-40) cc_final: 0.8655 (t0) REVERT: A 798 PHE cc_start: 0.8478 (t80) cc_final: 0.8230 (t80) REVERT: A 841 ARG cc_start: 0.7252 (ttp80) cc_final: 0.6943 (ttp80) REVERT: B 110 ARG cc_start: 0.8061 (ttt180) cc_final: 0.6284 (ptp90) REVERT: B 323 SER cc_start: 0.8412 (m) cc_final: 0.8176 (m) REVERT: B 486 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7642 (mm-30) REVERT: B 553 GLN cc_start: 0.7078 (mp10) cc_final: 0.6167 (mp10) REVERT: B 592 MET cc_start: 0.8306 (mmm) cc_final: 0.7966 (mmp) REVERT: B 606 GLU cc_start: 0.8319 (pp20) cc_final: 0.7840 (pp20) REVERT: B 611 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7788 (mm-30) REVERT: B 628 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7816 (mt-10) REVERT: B 649 GLU cc_start: 0.8027 (mp0) cc_final: 0.7482 (mp0) REVERT: B 674 TYR cc_start: 0.8291 (m-80) cc_final: 0.7961 (m-80) REVERT: B 688 MET cc_start: 0.7783 (mtt) cc_final: 0.6484 (tmm) REVERT: B 784 TYR cc_start: 0.8044 (t80) cc_final: 0.7799 (t80) REVERT: B 790 ASN cc_start: 0.9075 (m-40) cc_final: 0.8729 (t0) REVERT: B 798 PHE cc_start: 0.8507 (t80) cc_final: 0.8254 (t80) REVERT: B 841 ARG cc_start: 0.7223 (ttp80) cc_final: 0.6928 (ttp80) REVERT: C 110 ARG cc_start: 0.8060 (ttt180) cc_final: 0.6284 (ptp90) REVERT: C 323 SER cc_start: 0.8414 (m) cc_final: 0.8175 (m) REVERT: C 486 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7645 (mm-30) REVERT: C 553 GLN cc_start: 0.7065 (mp10) cc_final: 0.6159 (mp10) REVERT: C 592 MET cc_start: 0.8305 (mmm) cc_final: 0.7968 (mmp) REVERT: C 606 GLU cc_start: 0.8296 (pp20) cc_final: 0.7831 (pp20) REVERT: C 628 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 674 TYR cc_start: 0.8293 (m-80) cc_final: 0.7963 (m-80) REVERT: C 688 MET cc_start: 0.7772 (mtt) cc_final: 0.6473 (tmm) REVERT: C 784 TYR cc_start: 0.8060 (t80) cc_final: 0.7812 (t80) REVERT: C 790 ASN cc_start: 0.9096 (m-40) cc_final: 0.8743 (t0) REVERT: C 798 PHE cc_start: 0.8477 (t80) cc_final: 0.8225 (t80) REVERT: C 841 ARG cc_start: 0.7180 (ttp80) cc_final: 0.6868 (ttp80) REVERT: D 110 ARG cc_start: 0.8061 (ttt180) cc_final: 0.6282 (ptp90) REVERT: D 323 SER cc_start: 0.8415 (m) cc_final: 0.8177 (m) REVERT: D 435 ASP cc_start: 0.8230 (m-30) cc_final: 0.7886 (m-30) REVERT: D 486 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7642 (mm-30) REVERT: D 553 GLN cc_start: 0.7058 (mp10) cc_final: 0.6152 (mp10) REVERT: D 592 MET cc_start: 0.8306 (mmm) cc_final: 0.7967 (mmp) REVERT: D 606 GLU cc_start: 0.8316 (pp20) cc_final: 0.7841 (pp20) REVERT: D 611 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7784 (mm-30) REVERT: D 628 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7823 (mt-10) REVERT: D 649 GLU cc_start: 0.8022 (mp0) cc_final: 0.7484 (mp0) REVERT: D 674 TYR cc_start: 0.8293 (m-80) cc_final: 0.7962 (m-80) REVERT: D 688 MET cc_start: 0.7784 (mtt) cc_final: 0.6484 (tmm) REVERT: D 784 TYR cc_start: 0.8052 (t80) cc_final: 0.7808 (t80) REVERT: D 790 ASN cc_start: 0.9099 (m-40) cc_final: 0.8750 (t0) REVERT: D 798 PHE cc_start: 0.8477 (t80) cc_final: 0.8225 (t80) REVERT: D 841 ARG cc_start: 0.7216 (ttp80) cc_final: 0.6926 (ttp80) REVERT: D 1068 MET cc_start: 0.5218 (ttt) cc_final: 0.4251 (mtt) outliers start: 105 outliers final: 76 residues processed: 831 average time/residue: 0.4495 time to fit residues: 603.0525 Evaluate side-chains 829 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 753 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 417 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 915 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 915 ASN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 793 ASP Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 896 GLU Chi-restraints excluded: chain D residue 915 ASN Chi-restraints excluded: chain D residue 975 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 191 optimal weight: 0.8980 chunk 245 optimal weight: 0.1980 chunk 190 optimal weight: 0.9990 chunk 283 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 335 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 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 501 GLN A 646 ASN A 732 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN C 646 ASN C 732 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 29552 Z= 0.186 Angle : 0.574 9.776 40032 Z= 0.298 Chirality : 0.042 0.173 4484 Planarity : 0.005 0.113 4928 Dihedral : 6.267 54.303 4588 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.34 % Favored : 91.54 % Rotamer: Outliers : 3.73 % Allowed : 19.89 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.85 (0.15), residues: 3392 helix: 0.36 (0.11), residues: 2204 sheet: -1.15 (0.39), residues: 196 loop : -2.45 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 516 HIS 0.004 0.001 HIS C 129 PHE 0.012 0.001 PHE C 921 TYR 0.016 0.001 TYR D 905 ARG 0.005 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 789 time to evaluate : 3.653 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: A 110 ARG cc_start: 0.8032 (ttt180) cc_final: 0.6296 (ptp90) REVERT: A 297 GLN cc_start: 0.8691 (pp30) cc_final: 0.8350 (pp30) REVERT: A 323 SER cc_start: 0.8255 (m) cc_final: 0.7916 (m) REVERT: A 435 ASP cc_start: 0.8225 (m-30) cc_final: 0.7885 (m-30) REVERT: A 553 GLN cc_start: 0.7099 (mp10) cc_final: 0.6134 (mp10) REVERT: A 606 GLU cc_start: 0.8322 (pp20) cc_final: 0.7859 (pp20) REVERT: A 607 GLU cc_start: 0.8526 (tp30) cc_final: 0.8207 (tp30) REVERT: A 628 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7828 (mt-10) REVERT: A 674 TYR cc_start: 0.8292 (m-80) cc_final: 0.7999 (m-80) REVERT: A 688 MET cc_start: 0.7697 (mtt) cc_final: 0.6440 (tmm) REVERT: A 785 PHE cc_start: 0.8396 (m-80) cc_final: 0.8078 (m-80) REVERT: A 790 ASN cc_start: 0.9104 (m-40) cc_final: 0.8569 (t0) REVERT: A 798 PHE cc_start: 0.8478 (t80) cc_final: 0.8213 (t80) REVERT: A 808 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8305 (mm) REVERT: A 841 ARG cc_start: 0.7237 (ttp80) cc_final: 0.6947 (ttp80) REVERT: A 955 LEU cc_start: 0.9233 (tp) cc_final: 0.8947 (tp) REVERT: B 110 ARG cc_start: 0.8048 (ttt180) cc_final: 0.6286 (ptp90) REVERT: B 297 GLN cc_start: 0.8656 (pp30) cc_final: 0.8325 (pp30) REVERT: B 323 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8176 (m) REVERT: B 435 ASP cc_start: 0.8252 (m-30) cc_final: 0.7921 (m-30) REVERT: B 553 GLN cc_start: 0.7113 (mp10) cc_final: 0.6155 (mp10) REVERT: B 628 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7806 (mt-10) REVERT: B 645 SER cc_start: 0.7097 (OUTLIER) cc_final: 0.6079 (t) REVERT: B 649 GLU cc_start: 0.8043 (mp0) cc_final: 0.7285 (mp0) REVERT: B 674 TYR cc_start: 0.8289 (m-80) cc_final: 0.7998 (m-80) REVERT: B 688 MET cc_start: 0.7690 (mtt) cc_final: 0.6458 (tmm) REVERT: B 777 TRP cc_start: 0.7744 (t-100) cc_final: 0.7334 (t-100) REVERT: B 784 TYR cc_start: 0.8074 (t80) cc_final: 0.7861 (t80) REVERT: B 790 ASN cc_start: 0.9022 (m-40) cc_final: 0.8701 (t0) REVERT: B 798 PHE cc_start: 0.8487 (t80) cc_final: 0.8218 (t80) REVERT: B 841 ARG cc_start: 0.7245 (ttp80) cc_final: 0.6969 (ttp80) REVERT: B 955 LEU cc_start: 0.9229 (tp) cc_final: 0.8944 (tp) REVERT: C 110 ARG cc_start: 0.8051 (ttt180) cc_final: 0.6288 (ptp90) REVERT: C 297 GLN cc_start: 0.8662 (pp30) cc_final: 0.8330 (pp30) REVERT: C 323 SER cc_start: 0.8441 (m) cc_final: 0.8175 (m) REVERT: C 435 ASP cc_start: 0.8248 (m-30) cc_final: 0.7915 (m-30) REVERT: C 553 GLN cc_start: 0.7107 (mp10) cc_final: 0.6166 (mp10) REVERT: C 628 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7825 (mt-10) REVERT: C 674 TYR cc_start: 0.8294 (m-80) cc_final: 0.7998 (m-80) REVERT: C 688 MET cc_start: 0.7691 (mtt) cc_final: 0.6440 (tmm) REVERT: C 784 TYR cc_start: 0.8073 (t80) cc_final: 0.7690 (t80) REVERT: C 790 ASN cc_start: 0.9070 (m-40) cc_final: 0.8733 (t0) REVERT: C 798 PHE cc_start: 0.8440 (t80) cc_final: 0.8156 (t80) REVERT: C 841 ARG cc_start: 0.7243 (ttp80) cc_final: 0.6953 (ttp80) REVERT: C 955 LEU cc_start: 0.9224 (tp) cc_final: 0.8937 (tp) REVERT: C 1068 MET cc_start: 0.4805 (ttt) cc_final: 0.3924 (mtm) REVERT: D 110 ARG cc_start: 0.8048 (ttt180) cc_final: 0.6286 (ptp90) REVERT: D 297 GLN cc_start: 0.8660 (pp30) cc_final: 0.8328 (pp30) REVERT: D 323 SER cc_start: 0.8443 (m) cc_final: 0.8175 (m) REVERT: D 435 ASP cc_start: 0.8247 (m-30) cc_final: 0.7918 (m-30) REVERT: D 553 GLN cc_start: 0.7102 (mp10) cc_final: 0.6163 (mp10) REVERT: D 613 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7680 (tm-30) REVERT: D 628 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7817 (mt-10) REVERT: D 645 SER cc_start: 0.7105 (OUTLIER) cc_final: 0.6098 (t) REVERT: D 649 GLU cc_start: 0.8041 (mp0) cc_final: 0.7295 (mp0) REVERT: D 674 TYR cc_start: 0.8290 (m-80) cc_final: 0.7997 (m-80) REVERT: D 688 MET cc_start: 0.7686 (mtt) cc_final: 0.6458 (tmm) REVERT: D 777 TRP cc_start: 0.7747 (t-100) cc_final: 0.7338 (t-100) REVERT: D 784 TYR cc_start: 0.8092 (t80) cc_final: 0.7875 (t80) REVERT: D 790 ASN cc_start: 0.9070 (m-40) cc_final: 0.8743 (t0) REVERT: D 798 PHE cc_start: 0.8467 (t80) cc_final: 0.8186 (t80) REVERT: D 841 ARG cc_start: 0.7246 (ttp80) cc_final: 0.6969 (ttp80) REVERT: D 955 LEU cc_start: 0.9235 (tp) cc_final: 0.8948 (tp) REVERT: D 1068 MET cc_start: 0.5003 (ttt) cc_final: 0.4067 (mtt) outliers start: 116 outliers final: 83 residues processed: 839 average time/residue: 0.4022 time to fit residues: 537.2141 Evaluate side-chains 835 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 748 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 915 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 915 ASN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 793 ASP Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 915 ASN Chi-restraints excluded: chain D residue 975 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 213 optimal weight: 0.6980 chunk 228 optimal weight: 0.0770 chunk 165 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 263 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 732 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 29552 Z= 0.178 Angle : 0.575 10.839 40032 Z= 0.296 Chirality : 0.042 0.176 4484 Planarity : 0.005 0.109 4928 Dihedral : 6.180 55.945 4588 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.61 % Favored : 92.28 % Rotamer: Outliers : 3.41 % Allowed : 20.37 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.65 (0.15), residues: 3392 helix: 0.49 (0.11), residues: 2168 sheet: -1.06 (0.39), residues: 196 loop : -2.24 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 516 HIS 0.003 0.001 HIS C 129 PHE 0.015 0.001 PHE A 921 TYR 0.014 0.001 TYR B 905 ARG 0.005 0.000 ARG C 832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 783 time to evaluate : 3.532 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: A 110 ARG cc_start: 0.8025 (ttt180) cc_final: 0.6265 (ptp90) REVERT: A 297 GLN cc_start: 0.8681 (pp30) cc_final: 0.8325 (pp30) REVERT: A 435 ASP cc_start: 0.8211 (m-30) cc_final: 0.7900 (m-30) REVERT: A 486 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 553 GLN cc_start: 0.7090 (mp10) cc_final: 0.6128 (mp10) REVERT: A 606 GLU cc_start: 0.8291 (pp20) cc_final: 0.7804 (pp20) REVERT: A 607 GLU cc_start: 0.8540 (tp30) cc_final: 0.8194 (tp30) REVERT: A 628 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 649 GLU cc_start: 0.8295 (mp0) cc_final: 0.8012 (mp0) REVERT: A 658 GLN cc_start: 0.7665 (mp10) cc_final: 0.7158 (mp10) REVERT: A 674 TYR cc_start: 0.8283 (m-80) cc_final: 0.7983 (m-80) REVERT: A 688 MET cc_start: 0.7691 (mtt) cc_final: 0.6432 (tmm) REVERT: A 785 PHE cc_start: 0.8390 (m-80) cc_final: 0.8079 (m-80) REVERT: A 790 ASN cc_start: 0.9042 (m-40) cc_final: 0.8540 (t0) REVERT: A 798 PHE cc_start: 0.8474 (t80) cc_final: 0.8205 (t80) REVERT: A 808 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8248 (mm) REVERT: A 841 ARG cc_start: 0.7162 (ttp80) cc_final: 0.6881 (ttp80) REVERT: A 955 LEU cc_start: 0.9228 (tp) cc_final: 0.8954 (tp) REVERT: B 110 ARG cc_start: 0.8041 (ttt180) cc_final: 0.6277 (ptp90) REVERT: B 122 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7765 (t0) REVERT: B 297 GLN cc_start: 0.8660 (pp30) cc_final: 0.8301 (pp30) REVERT: B 323 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.8043 (m) REVERT: B 435 ASP cc_start: 0.8230 (m-30) cc_final: 0.7931 (m-30) REVERT: B 486 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 606 GLU cc_start: 0.8329 (pp20) cc_final: 0.7856 (pp20) REVERT: B 628 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7802 (mt-10) REVERT: B 645 SER cc_start: 0.6915 (OUTLIER) cc_final: 0.5879 (t) REVERT: B 649 GLU cc_start: 0.8067 (mp0) cc_final: 0.7324 (mp0) REVERT: B 674 TYR cc_start: 0.8282 (m-80) cc_final: 0.7976 (m-80) REVERT: B 688 MET cc_start: 0.7671 (mtt) cc_final: 0.6425 (tmm) REVERT: B 784 TYR cc_start: 0.8076 (t80) cc_final: 0.7639 (t80) REVERT: B 790 ASN cc_start: 0.9015 (m-40) cc_final: 0.8625 (t0) REVERT: B 798 PHE cc_start: 0.8488 (t80) cc_final: 0.8216 (t80) REVERT: B 841 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6915 (ttp80) REVERT: B 955 LEU cc_start: 0.9227 (tp) cc_final: 0.8951 (tp) REVERT: C 110 ARG cc_start: 0.8041 (ttt180) cc_final: 0.6276 (ptp90) REVERT: C 122 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7767 (t0) REVERT: C 297 GLN cc_start: 0.8666 (pp30) cc_final: 0.8299 (pp30) REVERT: C 435 ASP cc_start: 0.8227 (m-30) cc_final: 0.7926 (m-30) REVERT: C 486 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7657 (mm-30) REVERT: C 553 GLN cc_start: 0.7163 (mp10) cc_final: 0.6207 (mp10) REVERT: C 628 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7802 (mt-10) REVERT: C 649 GLU cc_start: 0.8258 (mp0) cc_final: 0.7964 (mp0) REVERT: C 674 TYR cc_start: 0.8281 (m-80) cc_final: 0.7978 (m-80) REVERT: C 688 MET cc_start: 0.7686 (mtt) cc_final: 0.6431 (tmm) REVERT: C 784 TYR cc_start: 0.8075 (t80) cc_final: 0.7608 (t80) REVERT: C 790 ASN cc_start: 0.9061 (m-40) cc_final: 0.8616 (t0) REVERT: C 798 PHE cc_start: 0.8434 (t80) cc_final: 0.8131 (t80) REVERT: C 841 ARG cc_start: 0.7169 (ttp80) cc_final: 0.6888 (ttp80) REVERT: C 955 LEU cc_start: 0.9223 (tp) cc_final: 0.8933 (tp) REVERT: C 1068 MET cc_start: 0.4452 (ttt) cc_final: 0.3618 (mtm) REVERT: D 110 ARG cc_start: 0.8039 (ttt180) cc_final: 0.6273 (ptp90) REVERT: D 122 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7764 (t0) REVERT: D 297 GLN cc_start: 0.8668 (pp30) cc_final: 0.8303 (pp30) REVERT: D 323 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8051 (m) REVERT: D 435 ASP cc_start: 0.8235 (m-30) cc_final: 0.7945 (m-30) REVERT: D 486 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7645 (mm-30) REVERT: D 553 GLN cc_start: 0.7166 (mp10) cc_final: 0.6209 (mp10) REVERT: D 606 GLU cc_start: 0.8333 (pp20) cc_final: 0.7853 (pp20) REVERT: D 628 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7819 (mt-10) REVERT: D 645 SER cc_start: 0.6861 (OUTLIER) cc_final: 0.5814 (t) REVERT: D 649 GLU cc_start: 0.8033 (mp0) cc_final: 0.7297 (mp0) REVERT: D 674 TYR cc_start: 0.8282 (m-80) cc_final: 0.8021 (m-80) REVERT: D 688 MET cc_start: 0.7670 (mtt) cc_final: 0.6426 (tmm) REVERT: D 784 TYR cc_start: 0.8089 (t80) cc_final: 0.7633 (t80) REVERT: D 790 ASN cc_start: 0.9064 (m-40) cc_final: 0.8631 (t0) REVERT: D 798 PHE cc_start: 0.8437 (t80) cc_final: 0.8132 (t80) REVERT: D 841 ARG cc_start: 0.7199 (ttp80) cc_final: 0.6933 (ttp80) REVERT: D 955 LEU cc_start: 0.9233 (tp) cc_final: 0.8937 (tp) REVERT: D 1068 MET cc_start: 0.5003 (ttt) cc_final: 0.4163 (mtt) outliers start: 106 outliers final: 87 residues processed: 840 average time/residue: 0.4043 time to fit residues: 546.0527 Evaluate side-chains 857 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 762 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 915 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 732 ASN Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 915 ASN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 793 ASP Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 915 ASN Chi-restraints excluded: chain D residue 975 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 0.9980 chunk 321 optimal weight: 0.6980 chunk 293 optimal weight: 0.5980 chunk 312 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 245 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 295 optimal weight: 0.9990 chunk 311 optimal weight: 0.6980 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 646 ASN A 732 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 ASN C 732 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29552 Z= 0.188 Angle : 0.582 10.792 40032 Z= 0.300 Chirality : 0.043 0.356 4484 Planarity : 0.004 0.105 4928 Dihedral : 6.138 58.042 4588 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.49 % Favored : 92.39 % Rotamer: Outliers : 3.44 % Allowed : 20.63 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.57 (0.15), residues: 3392 helix: 0.55 (0.11), residues: 2172 sheet: -1.03 (0.40), residues: 196 loop : -2.18 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 516 HIS 0.003 0.001 HIS C 129 PHE 0.011 0.001 PHE D 921 TYR 0.014 0.001 TYR D 905 ARG 0.005 0.000 ARG D 832 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 786 time to evaluate : 3.460 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: A 110 ARG cc_start: 0.8056 (ttt180) cc_final: 0.6296 (ptp90) REVERT: A 297 GLN cc_start: 0.8651 (pp30) cc_final: 0.8292 (pp30) REVERT: A 435 ASP cc_start: 0.8222 (m-30) cc_final: 0.7890 (m-30) REVERT: A 486 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 553 GLN cc_start: 0.7137 (mp10) cc_final: 0.6195 (mp10) REVERT: A 607 GLU cc_start: 0.8530 (tp30) cc_final: 0.8166 (tp30) REVERT: A 628 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 674 TYR cc_start: 0.8273 (m-80) cc_final: 0.8010 (m-80) REVERT: A 688 MET cc_start: 0.7663 (mtt) cc_final: 0.6404 (tmm) REVERT: A 785 PHE cc_start: 0.8347 (m-80) cc_final: 0.8055 (m-80) REVERT: A 790 ASN cc_start: 0.9037 (m-40) cc_final: 0.8549 (t0) REVERT: A 798 PHE cc_start: 0.8486 (t80) cc_final: 0.8203 (t80) REVERT: A 808 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 841 ARG cc_start: 0.7192 (ttp80) cc_final: 0.6919 (ttp80) REVERT: A 955 LEU cc_start: 0.9232 (tp) cc_final: 0.8989 (tp) REVERT: B 110 ARG cc_start: 0.8034 (ttt180) cc_final: 0.6266 (ptp90) REVERT: B 122 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7783 (t0) REVERT: B 297 GLN cc_start: 0.8630 (pp30) cc_final: 0.8267 (pp30) REVERT: B 435 ASP cc_start: 0.8229 (m-30) cc_final: 0.7916 (m-30) REVERT: B 486 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7659 (mm-30) REVERT: B 553 GLN cc_start: 0.7143 (mp10) cc_final: 0.6190 (mp10) REVERT: B 600 ASN cc_start: 0.8237 (m110) cc_final: 0.7895 (m-40) REVERT: B 628 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7794 (mt-10) REVERT: B 645 SER cc_start: 0.6821 (OUTLIER) cc_final: 0.5795 (t) REVERT: B 649 GLU cc_start: 0.8046 (mp0) cc_final: 0.7309 (mp0) REVERT: B 674 TYR cc_start: 0.8269 (m-80) cc_final: 0.8003 (m-80) REVERT: B 688 MET cc_start: 0.7668 (mtt) cc_final: 0.6416 (tmm) REVERT: B 784 TYR cc_start: 0.8086 (t80) cc_final: 0.7669 (t80) REVERT: B 790 ASN cc_start: 0.8995 (m-40) cc_final: 0.8672 (t0) REVERT: B 798 PHE cc_start: 0.8483 (t80) cc_final: 0.8206 (t80) REVERT: B 841 ARG cc_start: 0.7209 (ttp80) cc_final: 0.6950 (ttp80) REVERT: B 955 LEU cc_start: 0.9230 (tp) cc_final: 0.8942 (tp) REVERT: C 110 ARG cc_start: 0.8032 (ttt180) cc_final: 0.6265 (ptp90) REVERT: C 122 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7779 (t0) REVERT: C 297 GLN cc_start: 0.8636 (pp30) cc_final: 0.8273 (pp30) REVERT: C 435 ASP cc_start: 0.8227 (m-30) cc_final: 0.7913 (m-30) REVERT: C 486 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7643 (mm-30) REVERT: C 553 GLN cc_start: 0.7136 (mp10) cc_final: 0.6195 (mp10) REVERT: C 628 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7797 (mt-10) REVERT: C 674 TYR cc_start: 0.8273 (m-80) cc_final: 0.8008 (m-80) REVERT: C 688 MET cc_start: 0.7672 (mtt) cc_final: 0.6401 (tmm) REVERT: C 784 TYR cc_start: 0.8093 (t80) cc_final: 0.7657 (t80) REVERT: C 790 ASN cc_start: 0.9003 (m-40) cc_final: 0.8649 (t0) REVERT: C 841 ARG cc_start: 0.7195 (ttp80) cc_final: 0.6927 (ttp80) REVERT: C 955 LEU cc_start: 0.9230 (tp) cc_final: 0.8987 (tp) REVERT: C 1068 MET cc_start: 0.4463 (ttt) cc_final: 0.3774 (mtt) REVERT: D 110 ARG cc_start: 0.8031 (ttt180) cc_final: 0.6263 (ptp90) REVERT: D 122 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7761 (t0) REVERT: D 297 GLN cc_start: 0.8648 (pp30) cc_final: 0.8290 (pp30) REVERT: D 323 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.8035 (m) REVERT: D 435 ASP cc_start: 0.8229 (m-30) cc_final: 0.7917 (m-30) REVERT: D 486 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7659 (mm-30) REVERT: D 553 GLN cc_start: 0.7129 (mp10) cc_final: 0.6196 (mp10) REVERT: D 628 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7807 (mt-10) REVERT: D 645 SER cc_start: 0.6832 (OUTLIER) cc_final: 0.5810 (t) REVERT: D 649 GLU cc_start: 0.8046 (mp0) cc_final: 0.7312 (mp0) REVERT: D 674 TYR cc_start: 0.8272 (m-80) cc_final: 0.8003 (m-80) REVERT: D 688 MET cc_start: 0.7669 (mtt) cc_final: 0.6416 (tmm) REVERT: D 784 TYR cc_start: 0.8109 (t80) cc_final: 0.7681 (t80) REVERT: D 790 ASN cc_start: 0.9016 (m-40) cc_final: 0.8662 (t0) REVERT: D 841 ARG cc_start: 0.7221 (ttp80) cc_final: 0.6966 (ttp80) REVERT: D 955 LEU cc_start: 0.9234 (tp) cc_final: 0.8946 (tp) REVERT: D 1068 MET cc_start: 0.5022 (ttt) cc_final: 0.4113 (mtt) outliers start: 107 outliers final: 89 residues processed: 839 average time/residue: 0.4455 time to fit residues: 601.0757 Evaluate side-chains 837 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 741 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 915 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 915 ASN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 793 ASP Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 915 ASN Chi-restraints excluded: chain D residue 975 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.5980 chunk 330 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 229 optimal weight: 0.9990 chunk 346 optimal weight: 7.9990 chunk 319 optimal weight: 1.9990 chunk 276 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 732 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29552 Z= 0.183 Angle : 0.595 10.798 40032 Z= 0.303 Chirality : 0.043 0.300 4484 Planarity : 0.004 0.102 4928 Dihedral : 6.103 59.731 4588 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.52 % Favored : 92.36 % Rotamer: Outliers : 3.02 % Allowed : 21.88 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.56 (0.15), residues: 3392 helix: 0.56 (0.11), residues: 2200 sheet: -1.01 (0.40), residues: 196 loop : -2.27 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 516 HIS 0.004 0.001 HIS C 835 PHE 0.016 0.001 PHE B 921 TYR 0.017 0.001 TYR C 905 ARG 0.008 0.000 ARG D 832 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 753 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.8042 (ttt180) cc_final: 0.6287 (ptp90) REVERT: A 297 GLN cc_start: 0.8640 (pp30) cc_final: 0.8290 (pp30) REVERT: A 435 ASP cc_start: 0.8215 (m-30) cc_final: 0.7889 (m-30) REVERT: A 486 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7680 (mm-30) REVERT: A 553 GLN cc_start: 0.7102 (mp10) cc_final: 0.6180 (mp10) REVERT: A 607 GLU cc_start: 0.8539 (tp30) cc_final: 0.8139 (tp30) REVERT: A 613 GLU cc_start: 0.7801 (tt0) cc_final: 0.7493 (tm-30) REVERT: A 628 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7797 (mt-10) REVERT: A 674 TYR cc_start: 0.8249 (m-80) cc_final: 0.7978 (m-80) REVERT: A 688 MET cc_start: 0.7657 (mtt) cc_final: 0.6396 (tmm) REVERT: A 785 PHE cc_start: 0.8347 (m-80) cc_final: 0.8051 (m-80) REVERT: A 790 ASN cc_start: 0.9001 (m-40) cc_final: 0.8550 (t0) REVERT: A 798 PHE cc_start: 0.8459 (t80) cc_final: 0.8171 (t80) REVERT: A 808 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8258 (mm) REVERT: A 841 ARG cc_start: 0.7161 (ttp80) cc_final: 0.6897 (ttp80) REVERT: A 851 GLN cc_start: 0.8303 (mt0) cc_final: 0.8011 (mt0) REVERT: A 955 LEU cc_start: 0.9229 (tp) cc_final: 0.8945 (tp) REVERT: B 110 ARG cc_start: 0.8025 (ttt180) cc_final: 0.6256 (ptp90) REVERT: B 122 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7741 (t0) REVERT: B 297 GLN cc_start: 0.8597 (pp30) cc_final: 0.8239 (pp30) REVERT: B 435 ASP cc_start: 0.8223 (m-30) cc_final: 0.7911 (m-30) REVERT: B 486 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7743 (mm-30) REVERT: B 553 GLN cc_start: 0.7193 (mp10) cc_final: 0.6220 (mp10) REVERT: B 600 ASN cc_start: 0.8230 (m110) cc_final: 0.7890 (m-40) REVERT: B 628 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7793 (mt-10) REVERT: B 645 SER cc_start: 0.6816 (OUTLIER) cc_final: 0.5785 (t) REVERT: B 649 GLU cc_start: 0.8061 (mp0) cc_final: 0.7314 (mp0) REVERT: B 674 TYR cc_start: 0.8247 (m-80) cc_final: 0.7965 (m-80) REVERT: B 688 MET cc_start: 0.7663 (mtt) cc_final: 0.6412 (tmm) REVERT: B 784 TYR cc_start: 0.8078 (t80) cc_final: 0.7692 (t80) REVERT: B 790 ASN cc_start: 0.9016 (m-40) cc_final: 0.8718 (t0) REVERT: B 841 ARG cc_start: 0.7151 (ttp80) cc_final: 0.6891 (ttp80) REVERT: C 110 ARG cc_start: 0.8024 (ttt180) cc_final: 0.6255 (ptp90) REVERT: C 122 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7745 (t0) REVERT: C 297 GLN cc_start: 0.8601 (pp30) cc_final: 0.8243 (pp30) REVERT: C 435 ASP cc_start: 0.8281 (m-30) cc_final: 0.7985 (m-30) REVERT: C 486 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7657 (mm-30) REVERT: C 553 GLN cc_start: 0.7168 (mp10) cc_final: 0.6218 (mp10) REVERT: C 628 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7794 (mt-10) REVERT: C 674 TYR cc_start: 0.8251 (m-80) cc_final: 0.7970 (m-80) REVERT: C 688 MET cc_start: 0.7650 (mtt) cc_final: 0.6395 (tmm) REVERT: C 784 TYR cc_start: 0.8077 (t80) cc_final: 0.7655 (t80) REVERT: C 790 ASN cc_start: 0.9004 (m-40) cc_final: 0.8659 (t0) REVERT: C 841 ARG cc_start: 0.7143 (ttp80) cc_final: 0.6876 (ttp80) REVERT: C 851 GLN cc_start: 0.8291 (mt0) cc_final: 0.7998 (mt0) REVERT: C 1068 MET cc_start: 0.4523 (ttt) cc_final: 0.3861 (mtt) REVERT: D 110 ARG cc_start: 0.8023 (ttt180) cc_final: 0.6255 (ptp90) REVERT: D 122 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7741 (t0) REVERT: D 297 GLN cc_start: 0.8601 (pp30) cc_final: 0.8245 (pp30) REVERT: D 323 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.7800 (m) REVERT: D 435 ASP cc_start: 0.8220 (m-30) cc_final: 0.7895 (m-30) REVERT: D 486 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7744 (mm-30) REVERT: D 553 GLN cc_start: 0.7116 (mp10) cc_final: 0.6174 (mp10) REVERT: D 613 GLU cc_start: 0.7553 (tt0) cc_final: 0.7324 (tt0) REVERT: D 628 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7789 (mt-10) REVERT: D 645 SER cc_start: 0.6818 (OUTLIER) cc_final: 0.5794 (t) REVERT: D 649 GLU cc_start: 0.8062 (mp0) cc_final: 0.7324 (mp0) REVERT: D 674 TYR cc_start: 0.8247 (m-80) cc_final: 0.7966 (m-80) REVERT: D 688 MET cc_start: 0.7664 (mtt) cc_final: 0.6410 (tmm) REVERT: D 784 TYR cc_start: 0.8088 (t80) cc_final: 0.7673 (t80) REVERT: D 790 ASN cc_start: 0.9015 (m-40) cc_final: 0.8668 (t0) REVERT: D 841 ARG cc_start: 0.7158 (ttp80) cc_final: 0.6902 (ttp80) REVERT: D 851 GLN cc_start: 0.8289 (mt0) cc_final: 0.8000 (mt0) REVERT: D 1068 MET cc_start: 0.5010 (ttt) cc_final: 0.4091 (mtt) outliers start: 94 outliers final: 85 residues processed: 802 average time/residue: 0.4209 time to fit residues: 545.8953 Evaluate side-chains 830 residues out of total 3112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 738 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 915 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 732 ASN Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 915 ASN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 793 ASP Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 915 ASN Chi-restraints excluded: chain D residue 975 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 3.9990 chunk 294 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 76 optimal weight: 0.1980 chunk 276 optimal weight: 0.0060 chunk 115 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 732 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126655 restraints weight = 44038.135| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.87 r_work: 0.3305 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.304 29552 Z= 0.355 Angle : 0.813 59.199 40032 Z= 0.463 Chirality : 0.042 0.262 4484 Planarity : 0.004 0.100 4928 Dihedral : 6.093 59.747 4588 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.55 % Favored : 92.33 % Rotamer: Outliers : 3.15 % Allowed : 21.72 % Favored : 75.13 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.55 (0.15), residues: 3392 helix: 0.56 (0.11), residues: 2200 sheet: -1.00 (0.40), residues: 196 loop : -2.26 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 516 HIS 0.004 0.001 HIS C 835 PHE 0.012 0.001 PHE D 829 TYR 0.016 0.001 TYR C 905 ARG 0.011 0.000 ARG D 832 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9032.19 seconds wall clock time: 163 minutes 37.07 seconds (9817.07 seconds total)