Starting phenix.real_space_refine on Mon Mar 25 12:47:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4q_23664/03_2024/7m4q_23664_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4q_23664/03_2024/7m4q_23664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4q_23664/03_2024/7m4q_23664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4q_23664/03_2024/7m4q_23664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4q_23664/03_2024/7m4q_23664_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4q_23664/03_2024/7m4q_23664_trim_updated.pdb" } resolution = 2.87 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 ------------------------------------------------------------------------------- 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= 0.203 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 102 5.16 5 C 15619 2.51 5 N 3978 2.21 5 O 4523 1.98 5 H 24342 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 66": "OE1" <-> "OE2" Residue "A ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 524": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A ARG 651": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A ARG 718": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A ARG 752": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 898": "OE1" <-> "OE2" Residue "A GLU 959": "OE1" <-> "OE2" Residue "A GLU 969": "OE1" <-> "OE2" Residue "A ARG 984": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B ARG 524": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 535": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 695": "OE1" <-> "OE2" Residue "B ARG 713": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 752": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 798": "OE1" <-> "OE2" Residue "B GLU 809": "OE1" <-> "OE2" Residue "B GLU 863": "OE1" <-> "OE2" Residue "B GLU 873": "OE1" <-> "OE2" Residue "B GLU 959": "OE1" <-> "OE2" Residue "B GLU 966": "OE1" <-> "OE2" Residue "B GLU 969": "OE1" <-> "OE2" Residue "B ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1041": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 513": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 535": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 568": "OE1" <-> "OE2" Residue "C GLU 569": "OE1" <-> "OE2" Residue "C GLU 608": "OE1" <-> "OE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 638": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 713": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 718": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 752": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 781": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 816": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 818": "OE1" <-> "OE2" Residue "C ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 863": "OE1" <-> "OE2" Residue "C GLU 870": "OE1" <-> "OE2" Residue "C PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 959": "OE1" <-> "OE2" Residue "C GLU 963": "OE1" <-> "OE2" Residue "C ARG 984": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48572 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 16127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 16127 Classifications: {'peptide': 1049} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 48, 'TRANS': 1000} Chain: "B" Number of atoms: 16090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 16090 Classifications: {'peptide': 1047} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 47, 'TRANS': 999} Chain: "C" Number of atoms: 16069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 16069 Classifications: {'peptide': 1046} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 47, 'TRANS': 998} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 142 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 62 Chain: "C" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 144 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 62 Time building chain proxies: 20.37, per 1000 atoms: 0.42 Number of scatterers: 48572 At special positions: 0 Unit cell: (129.6, 125.28, 157.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 8 15.00 O 4523 8.00 N 3978 7.00 C 15619 6.00 H 24342 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 36.18 Conformation dependent library (CDL) restraints added in 5.7 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 113 helices and 27 sheets defined 55.2% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.82 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 27 Processing helix chain 'A' and resid 54 through 68 removed outlier: 5.291A pdb=" N GLN A 63 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 116 removed outlier: 4.412A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 163 through 166 No H-bonds generated for 'chain 'A' and resid 163 through 166' Processing helix chain 'A' and resid 190 through 196 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 299 through 316 removed outlier: 4.203A pdb=" N LYS A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 358 Processing helix chain 'A' and resid 362 through 386 Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 423 removed outlier: 4.227A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 458 removed outlier: 5.551A pdb=" N GLY A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 4.763A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 496 removed outlier: 3.840A pdb=" N ILE A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 510 through 538 removed outlier: 3.782A pdb=" N PHE A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 558 Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 645 through 658 removed outlier: 3.695A pdb=" N ALA A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN A 656 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N MET A 657 " --> pdb=" O MET A 653 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 658 " --> pdb=" O ALA A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.622A pdb=" N GLN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 744 through 756 Processing helix chain 'A' and resid 778 through 780 No H-bonds generated for 'chain 'A' and resid 778 through 780' Processing helix chain 'A' and resid 784 through 789 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 838 through 855 removed outlier: 3.637A pdb=" N LEU A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Proline residue: A 853 - end of helix Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 873 through 897 removed outlier: 3.892A pdb=" N ALA A 878 " --> pdb=" O SER A 874 " (cutoff:3.500A) Proline residue: A 879 - end of helix Processing helix chain 'A' and resid 902 through 928 removed outlier: 5.268A pdb=" N VAL A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL A 910 " --> pdb=" O VAL A 906 " (cutoff:3.500A) Proline residue: A 911 - end of helix removed outlier: 3.743A pdb=" N GLY A 916 " --> pdb=" O LEU A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 933 No H-bonds generated for 'chain 'A' and resid 931 through 933' Processing helix chain 'A' and resid 937 through 967 removed outlier: 3.690A pdb=" N LEU A 956 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 1001 removed outlier: 3.808A pdb=" N LEU A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Proline residue: A 985 - end of helix Proline residue: A 999 - end of helix Processing helix chain 'A' and resid 1008 through 1043 removed outlier: 4.136A pdb=" N GLY A1017 " --> pdb=" O SER A1013 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE A1030 " --> pdb=" O THR A1026 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A1031 " --> pdb=" O PHE A1027 " (cutoff:3.500A) Proline residue: A1034 - end of helix Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.735A pdb=" N THR B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 68 removed outlier: 5.269A pdb=" N GLN B 63 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 removed outlier: 3.619A pdb=" N GLN B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 168 removed outlier: 4.369A pdb=" N LYS B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLU B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Proline residue: B 165 - end of helix removed outlier: 3.609A pdb=" N ARG B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 299 through 316 removed outlier: 4.245A pdb=" N LYS B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 358 Processing helix chain 'B' and resid 362 through 385 removed outlier: 4.141A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix removed outlier: 3.613A pdb=" N ILE B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 423 removed outlier: 4.212A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 456 removed outlier: 5.489A pdb=" N GLY B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 461 through 496 removed outlier: 3.691A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 510 through 537 removed outlier: 3.966A pdb=" N PHE B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 removed outlier: 3.802A pdb=" N GLN B 559 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 645 through 658 removed outlier: 3.698A pdb=" N ALA B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 710 removed outlier: 3.627A pdb=" N GLN B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 744 through 756 Processing helix chain 'B' and resid 778 through 781 Processing helix chain 'B' and resid 784 through 789 Processing helix chain 'B' and resid 802 through 804 No H-bonds generated for 'chain 'B' and resid 802 through 804' Processing helix chain 'B' and resid 838 through 851 Processing helix chain 'B' and resid 867 through 874 Processing helix chain 'B' and resid 878 through 897 Processing helix chain 'B' and resid 902 through 927 Proline residue: B 911 - end of helix removed outlier: 3.695A pdb=" N ILE B 915 " --> pdb=" O LEU B 912 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY B 916 " --> pdb=" O GLY B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 967 Processing helix chain 'B' and resid 971 through 1001 removed outlier: 4.736A pdb=" N ARG B 984 " --> pdb=" O LYS B 980 " (cutoff:3.500A) Proline residue: B 985 - end of helix Proline residue: B 999 - end of helix Processing helix chain 'B' and resid 1008 through 1043 removed outlier: 4.330A pdb=" N PHE B1031 " --> pdb=" O PHE B1027 " (cutoff:3.500A) Proline residue: B1034 - end of helix Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.717A pdb=" N HIS C 7 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.799A pdb=" N LYS C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 69 Processing helix chain 'C' and resid 100 through 117 removed outlier: 4.159A pdb=" N SER C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 removed outlier: 3.523A pdb=" N GLN C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 299 through 316 removed outlier: 3.998A pdb=" N LYS C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 358 Processing helix chain 'C' and resid 362 through 386 removed outlier: 3.751A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.921A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 405 removed outlier: 4.461A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 422 Processing helix chain 'C' and resid 427 through 452 removed outlier: 3.643A pdb=" N SER C 439 " --> pdb=" O MET C 435 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 458 Processing helix chain 'C' and resid 461 through 496 removed outlier: 3.679A pdb=" N GLN C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 510 through 538 Processing helix chain 'C' and resid 540 through 560 Processing helix chain 'C' and resid 586 through 601 Processing helix chain 'C' and resid 641 through 643 No H-bonds generated for 'chain 'C' and resid 641 through 643' Processing helix chain 'C' and resid 645 through 658 removed outlier: 4.029A pdb=" N LEU C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN C 656 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET C 657 " --> pdb=" O MET C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 676 No H-bonds generated for 'chain 'C' and resid 674 through 676' Processing helix chain 'C' and resid 694 through 709 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 744 through 756 Processing helix chain 'C' and resid 778 through 780 No H-bonds generated for 'chain 'C' and resid 778 through 780' Processing helix chain 'C' and resid 784 through 789 Processing helix chain 'C' and resid 802 through 804 No H-bonds generated for 'chain 'C' and resid 802 through 804' Processing helix chain 'C' and resid 838 through 851 Processing helix chain 'C' and resid 853 through 855 No H-bonds generated for 'chain 'C' and resid 853 through 855' Processing helix chain 'C' and resid 867 through 876 Processing helix chain 'C' and resid 878 through 897 Processing helix chain 'C' and resid 901 through 928 removed outlier: 3.639A pdb=" N VAL C 909 " --> pdb=" O SER C 905 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 910 " --> pdb=" O VAL C 906 " (cutoff:3.500A) Proline residue: C 911 - end of helix removed outlier: 3.949A pdb=" N GLY C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 917 " --> pdb=" O GLY C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 966 removed outlier: 3.763A pdb=" N ILE C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 996 removed outlier: 4.972A pdb=" N ARG C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) Proline residue: C 985 - end of helix Processing helix chain 'C' and resid 998 through 1001 No H-bonds generated for 'chain 'C' and resid 998 through 1001' Processing helix chain 'C' and resid 1008 through 1027 Processing helix chain 'C' and resid 1029 through 1043 Proline residue: C1034 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.072A pdb=" N GLN A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 77 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 322 through 328 removed outlier: 6.486A pdb=" N VAL A 139 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 Processing sheet with id= D, first strand: chain 'A' and resid 278 through 281 removed outlier: 6.770A pdb=" N LYS A 631 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE A 610 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 629 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR A 612 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 627 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N SER A 614 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 625 " --> pdb=" O SER A 614 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 825 through 830 Processing sheet with id= F, first strand: chain 'A' and resid 724 through 732 Processing sheet with id= G, first strand: chain 'A' and resid 762 through 765 Processing sheet with id= H, first strand: chain 'A' and resid 791 through 793 Processing sheet with id= I, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.718A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 128 through 131 removed outlier: 3.805A pdb=" N GLN B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 77 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 321 through 328 removed outlier: 6.390A pdb=" N VAL B 139 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 266 through 272 Processing sheet with id= M, first strand: chain 'B' and resid 279 through 281 Processing sheet with id= N, first strand: chain 'B' and resid 825 through 830 Processing sheet with id= O, first strand: chain 'B' and resid 725 through 732 Processing sheet with id= P, first strand: chain 'B' and resid 762 through 765 Processing sheet with id= Q, first strand: chain 'B' and resid 791 through 793 Processing sheet with id= R, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.863A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.724A pdb=" N GLN C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 322 through 328 removed outlier: 6.404A pdb=" N VAL C 139 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 266 through 272 Processing sheet with id= V, first strand: chain 'C' and resid 278 through 281 removed outlier: 6.707A pdb=" N LYS C 631 " --> pdb=" O GLU C 608 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE C 610 " --> pdb=" O PHE C 629 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE C 629 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR C 612 " --> pdb=" O ILE C 627 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE C 627 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER C 614 " --> pdb=" O ALA C 625 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA C 625 " --> pdb=" O SER C 614 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 682 through 687 removed outlier: 3.586A pdb=" N GLY C 830 " --> pdb=" O PHE C 682 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 725 through 729 Processing sheet with id= Y, first strand: chain 'C' and resid 762 through 765 Processing sheet with id= Z, first strand: chain 'C' and resid 791 through 793 Processing sheet with id= AA, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.675A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) 1376 hydrogen bonds defined for protein. 3975 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: 21.86 Time building geometry restraints manager: 37.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 24336 1.01 - 1.21: 252 1.21 - 1.41: 9579 1.41 - 1.61: 14660 1.61 - 1.81: 212 Bond restraints: 49039 Sorted by residual: bond pdb=" C ILE C 915 " pdb=" O ILE C 915 " ideal model delta sigma weight residual 1.237 1.143 0.094 1.17e-02 7.31e+03 6.45e+01 bond pdb=" C21 3PE C1104 " pdb=" O21 3PE C1104 " ideal model delta sigma weight residual 1.316 1.466 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C21 3PE B1101 " pdb=" O21 3PE B1101 " ideal model delta sigma weight residual 1.316 1.456 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C21 3PE B1104 " pdb=" O21 3PE B1104 " ideal model delta sigma weight residual 1.316 1.455 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C ILE C 78 " pdb=" O ILE C 78 " ideal model delta sigma weight residual 1.238 1.162 0.076 1.10e-02 8.26e+03 4.76e+01 ... (remaining 49034 not shown) Histogram of bond angle deviations from ideal: 74.97 - 86.96: 5 86.96 - 98.96: 3 98.96 - 110.95: 53437 110.95 - 122.94: 30554 122.94 - 134.94: 4706 Bond angle restraints: 88705 Sorted by residual: angle pdb=" H1 MET C 1 " pdb=" N MET C 1 " pdb=" H3 MET C 1 " ideal model delta sigma weight residual 109.47 74.97 34.50 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CA ALA A 974 " pdb=" CB ALA A 974 " pdb=" HB3 ALA A 974 " ideal model delta sigma weight residual 109.00 77.65 31.35 3.00e+00 1.11e-01 1.09e+02 angle pdb=" CA ALA A 974 " pdb=" CB ALA A 974 " pdb=" HB2 ALA A 974 " ideal model delta sigma weight residual 109.00 80.08 28.92 3.00e+00 1.11e-01 9.29e+01 angle pdb=" HB1 ALA A 974 " pdb=" CB ALA A 974 " pdb=" HB3 ALA A 974 " ideal model delta sigma weight residual 110.00 81.19 28.81 3.00e+00 1.11e-01 9.22e+01 angle pdb=" N ILE C 438 " pdb=" CA ILE C 438 " pdb=" C ILE C 438 " ideal model delta sigma weight residual 112.29 121.03 -8.74 9.40e-01 1.13e+00 8.65e+01 ... (remaining 88700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.29: 21513 24.29 - 48.58: 1296 48.58 - 72.87: 394 72.87 - 97.16: 19 97.16 - 121.46: 1 Dihedral angle restraints: 23223 sinusoidal: 12804 harmonic: 10419 Sorted by residual: dihedral pdb=" CA GLY C 221 " pdb=" C GLY C 221 " pdb=" N ALA C 222 " pdb=" CA ALA C 222 " ideal model delta harmonic sigma weight residual -180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ALA C 294 " pdb=" C ALA C 294 " pdb=" N THR C 295 " pdb=" CA THR C 295 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLY B 221 " pdb=" C GLY B 221 " pdb=" N ALA B 222 " pdb=" CA ALA B 222 " ideal model delta harmonic sigma weight residual -180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 23220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3561 0.103 - 0.205: 312 0.205 - 0.308: 34 0.308 - 0.410: 9 0.410 - 0.513: 2 Chirality restraints: 3918 Sorted by residual: chirality pdb=" CA GLU C 863 " pdb=" N GLU C 863 " pdb=" C GLU C 863 " pdb=" CB GLU C 863 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" CA TYR B 882 " pdb=" N TYR B 882 " pdb=" C TYR B 882 " pdb=" CB TYR B 882 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA GLU B 675 " pdb=" N GLU B 675 " pdb=" C GLU B 675 " pdb=" CB GLU B 675 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 3915 not shown) Planarity restraints: 7271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 935 " 0.321 2.00e-02 2.50e+03 3.55e-01 1.89e+03 pdb=" CG ASN B 935 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN B 935 " -0.301 2.00e-02 2.50e+03 pdb=" ND2 ASN B 935 " -0.009 2.00e-02 2.50e+03 pdb="HD21 ASN B 935 " 0.551 2.00e-02 2.50e+03 pdb="HD22 ASN B 935 " -0.508 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 644 " -0.213 2.00e-02 2.50e+03 2.59e-01 1.01e+03 pdb=" CD GLN C 644 " 0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN C 644 " 0.212 2.00e-02 2.50e+03 pdb=" NE2 GLN C 644 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN C 644 " 0.395 2.00e-02 2.50e+03 pdb="HE22 GLN C 644 " -0.395 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 829 " -0.216 2.00e-02 2.50e+03 2.56e-01 9.82e+02 pdb=" CD GLN B 829 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 829 " 0.209 2.00e-02 2.50e+03 pdb=" NE2 GLN B 829 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 829 " 0.387 2.00e-02 2.50e+03 pdb="HE22 GLN B 829 " -0.391 2.00e-02 2.50e+03 ... (remaining 7268 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 3587 2.20 - 2.80: 101320 2.80 - 3.40: 133577 3.40 - 4.00: 179047 4.00 - 4.60: 276822 Nonbonded interactions: 694353 Sorted by model distance: nonbonded pdb=" O SER B 238 " pdb="HE21 GLN C 734 " model vdw 1.603 1.850 nonbonded pdb=" O LEU B 676 " pdb="HD12 LEU B 676 " model vdw 1.615 2.620 nonbonded pdb=" O SER B1003 " pdb=" HE2 HIS B1012 " model vdw 1.619 1.850 nonbonded pdb=" O GLN B 308 " pdb=" HG SER B 311 " model vdw 1.623 1.850 nonbonded pdb=" O THR C 56 " pdb=" HG1 THR C 60 " model vdw 1.633 1.850 ... (remaining 694348 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' and (resid 1 through 575 or (resid 576 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG \ 1 or name HG21 or name HG22 or name HG23)) or resid 577 through 1046)) selection = (chain 'B' and resid 1 through 1046) selection = (chain 'C' and (resid 1 through 575 or (resid 576 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG \ 1 or name HG21 or name HG22 or name HG23)) or resid 577 through 1046)) } 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: 0.110 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: 0.740 Extract box with map and model: 3.470 Check model and map are aligned: 0.730 Set scattering table: 0.410 Process input model: 150.870 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 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 : 0.011 0.150 24697 Z= 0.699 Angle : 1.075 14.961 33522 Z= 0.636 Chirality : 0.064 0.513 3918 Planarity : 0.007 0.078 4275 Dihedral : 15.290 121.455 9053 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 2.63 % Allowed : 9.34 % Favored : 88.03 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3136 helix: 1.18 (0.12), residues: 1679 sheet: 0.09 (0.24), residues: 444 loop : -0.66 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 790 HIS 0.021 0.002 HIS C1012 PHE 0.037 0.003 PHE C 396 TYR 0.021 0.003 TYR B 938 ARG 0.013 0.001 ARG C 872 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 706 time to evaluate : 3.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6281 (ttt) cc_final: 0.5860 (tpp) REVERT: A 8 ARG cc_start: 0.7345 (mtt-85) cc_final: 0.7058 (mtt-85) REVERT: A 18 VAL cc_start: 0.7721 (t) cc_final: 0.7461 (m) REVERT: A 34 GLN cc_start: 0.7295 (tt0) cc_final: 0.7036 (tt0) REVERT: A 87 GLN cc_start: 0.8251 (mt0) cc_final: 0.8012 (mt0) REVERT: A 95 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6509 (mt-10) REVERT: A 101 ASP cc_start: 0.8123 (m-30) cc_final: 0.7845 (m-30) REVERT: A 112 GLN cc_start: 0.7956 (tt0) cc_final: 0.7539 (mt0) REVERT: A 155 LYS cc_start: 0.8405 (mttt) cc_final: 0.7883 (mtmm) REVERT: A 192 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7722 (mttm) REVERT: A 193 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7905 (mt) REVERT: A 201 SER cc_start: 0.8039 (m) cc_final: 0.7757 (m) REVERT: A 263 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7726 (ptpt) REVERT: A 284 LYS cc_start: 0.7393 (mttt) cc_final: 0.6972 (mmmm) REVERT: A 334 ARG cc_start: 0.6383 (tpp-160) cc_final: 0.6094 (ttm110) REVERT: A 338 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6605 (mt-10) REVERT: A 342 HIS cc_start: 0.5766 (t70) cc_final: 0.5178 (m-70) REVERT: A 346 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6007 (mt-10) REVERT: A 349 ILE cc_start: 0.6968 (mm) cc_final: 0.6388 (mt) REVERT: A 353 ILE cc_start: 0.6920 (mm) cc_final: 0.6663 (mt) REVERT: A 390 ILE cc_start: 0.7543 (mt) cc_final: 0.7284 (mm) REVERT: A 395 MET cc_start: 0.7411 (mmm) cc_final: 0.6544 (mmm) REVERT: A 407 ASP cc_start: 0.7013 (m-30) cc_final: 0.6655 (m-30) REVERT: A 408 ASP cc_start: 0.7109 (m-30) cc_final: 0.6663 (m-30) REVERT: A 410 ILE cc_start: 0.6514 (mm) cc_final: 0.6257 (mt) REVERT: A 429 THR cc_start: 0.7706 (m) cc_final: 0.7422 (t) REVERT: A 585 THR cc_start: 0.8228 (m) cc_final: 0.7985 (p) REVERT: A 601 MET cc_start: 0.7514 (mtm) cc_final: 0.7287 (mtp) REVERT: A 608 GLU cc_start: 0.6883 (tt0) cc_final: 0.6598 (tm-30) REVERT: A 642 GLU cc_start: 0.6353 (mt-10) cc_final: 0.5906 (mp0) REVERT: A 647 SER cc_start: 0.7571 (t) cc_final: 0.7155 (p) REVERT: A 653 MET cc_start: 0.6300 (mtp) cc_final: 0.5949 (mmt) REVERT: A 704 ILE cc_start: 0.7359 (mt) cc_final: 0.7096 (mm) REVERT: A 766 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7611 (mtm-85) REVERT: A 782 MET cc_start: 0.8413 (mmp) cc_final: 0.6708 (mmt) REVERT: A 823 VAL cc_start: 0.8277 (p) cc_final: 0.8072 (t) REVERT: A 842 MET cc_start: 0.6240 (mtm) cc_final: 0.5668 (mtm) REVERT: A 892 CYS cc_start: 0.6968 (m) cc_final: 0.6652 (m) REVERT: A 940 GLN cc_start: 0.6822 (mt0) cc_final: 0.6572 (mt0) REVERT: A 949 LEU cc_start: 0.7690 (tp) cc_final: 0.7402 (tm) REVERT: A 952 LYS cc_start: 0.6785 (tttt) cc_final: 0.6159 (ttpp) REVERT: A 960 PHE cc_start: 0.6259 (t80) cc_final: 0.5844 (t80) REVERT: A 984 ARG cc_start: 0.6130 (ttt90) cc_final: 0.5051 (ttt90) REVERT: A 1018 VAL cc_start: 0.7177 (OUTLIER) cc_final: 0.6812 (m) REVERT: A 1022 VAL cc_start: 0.7368 (p) cc_final: 0.7045 (m) REVERT: B 8 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7477 (mtt90) REVERT: B 20 MET cc_start: 0.6160 (mtt) cc_final: 0.5848 (tpp) REVERT: B 34 GLN cc_start: 0.7670 (tt0) cc_final: 0.7370 (tt0) REVERT: B 55 GLU cc_start: 0.7460 (tt0) cc_final: 0.6687 (mp0) REVERT: B 164 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6501 (mt-10) REVERT: B 184 MET cc_start: 0.8273 (tpp) cc_final: 0.8018 (tpp) REVERT: B 229 VAL cc_start: 0.8133 (p) cc_final: 0.7914 (m) REVERT: B 237 GLN cc_start: 0.7274 (tp40) cc_final: 0.6909 (tm130) REVERT: B 248 ASN cc_start: 0.8466 (m-40) cc_final: 0.8253 (m110) REVERT: B 269 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7067 (pp20) REVERT: B 304 GLU cc_start: 0.6406 (mt-10) cc_final: 0.6128 (mt-10) REVERT: B 308 GLN cc_start: 0.6066 (tt0) cc_final: 0.5724 (tm-30) REVERT: B 312 GLU cc_start: 0.6397 (mt-10) cc_final: 0.6173 (mm-30) REVERT: B 334 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6236 (ttt180) REVERT: B 363 ARG cc_start: 0.7272 (mtp85) cc_final: 0.6996 (mtt90) REVERT: B 366 ILE cc_start: 0.7942 (tt) cc_final: 0.7596 (tp) REVERT: B 395 MET cc_start: 0.7858 (mmt) cc_final: 0.7473 (mmt) REVERT: B 433 ARG cc_start: 0.6909 (tpt-90) cc_final: 0.6636 (tpp80) REVERT: B 435 MET cc_start: 0.7546 (mmm) cc_final: 0.7343 (mmm) REVERT: B 439 SER cc_start: 0.8153 (m) cc_final: 0.7945 (p) REVERT: B 468 ARG cc_start: 0.7399 (ttm110) cc_final: 0.7123 (ttp-110) REVERT: B 478 MET cc_start: 0.8239 (mmp) cc_final: 0.7848 (mmp) REVERT: B 530 GLN cc_start: 0.6714 (mt0) cc_final: 0.6105 (mt0) REVERT: B 536 MET cc_start: 0.6352 (ttm) cc_final: 0.6077 (ttt) REVERT: B 612 THR cc_start: 0.6734 (OUTLIER) cc_final: 0.6531 (p) REVERT: B 690 SER cc_start: 0.7949 (OUTLIER) cc_final: 0.7578 (p) REVERT: B 692 GLN cc_start: 0.7388 (mt0) cc_final: 0.7168 (mt0) REVERT: B 718 ARG cc_start: 0.6194 (ptt90) cc_final: 0.5822 (pmm-80) REVERT: B 749 ASN cc_start: 0.7541 (m-40) cc_final: 0.7276 (m-40) REVERT: B 751 MET cc_start: 0.8359 (ptt) cc_final: 0.8051 (ptt) REVERT: B 768 ARG cc_start: 0.6204 (mtp85) cc_final: 0.5808 (ttp80) REVERT: B 786 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: B 798 GLU cc_start: 0.6999 (mp0) cc_final: 0.6678 (mp0) REVERT: B 846 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7212 (mt-10) REVERT: B 862 TYR cc_start: 0.7975 (p90) cc_final: 0.7590 (p90) REVERT: B 872 ARG cc_start: 0.6727 (mmt90) cc_final: 0.6477 (mtt-85) REVERT: B 884 LEU cc_start: 0.8280 (mt) cc_final: 0.7953 (tt) REVERT: B 887 LEU cc_start: 0.8167 (tp) cc_final: 0.7761 (tm) REVERT: B 918 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7389 (mt) REVERT: B 949 LEU cc_start: 0.8188 (tp) cc_final: 0.7974 (tt) REVERT: B 964 LEU cc_start: 0.8118 (mt) cc_final: 0.7858 (mp) REVERT: B 987 ILE cc_start: 0.8041 (mt) cc_final: 0.7830 (mm) REVERT: B 998 LEU cc_start: 0.8052 (tt) cc_final: 0.7850 (tm) REVERT: B 1023 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7278 (mm) REVERT: B 1028 LEU cc_start: 0.6739 (mt) cc_final: 0.6533 (mt) REVERT: B 1045 LYS cc_start: 0.6905 (mmmt) cc_final: 0.6634 (mttm) REVERT: C 20 MET cc_start: 0.8221 (mtp) cc_final: 0.7953 (mtp) REVERT: C 34 GLN cc_start: 0.7494 (tt0) cc_final: 0.7260 (tt0) REVERT: C 66 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6523 (mt-10) REVERT: C 67 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: C 124 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.7006 (mtt-85) REVERT: C 188 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8467 (mt) REVERT: C 192 LYS cc_start: 0.7699 (mttt) cc_final: 0.7353 (mtpt) REVERT: C 197 GLN cc_start: 0.7700 (mp10) cc_final: 0.7082 (mp-120) REVERT: C 244 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6922 (mp0) REVERT: C 261 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7298 (mmm160) REVERT: C 269 GLU cc_start: 0.8306 (pt0) cc_final: 0.7956 (pt0) REVERT: C 314 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7146 (mtm110) REVERT: C 329 THR cc_start: 0.8245 (m) cc_final: 0.7804 (p) REVERT: C 346 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6800 (mt-10) REVERT: C 370 LEU cc_start: 0.8474 (mt) cc_final: 0.8229 (mp) REVERT: C 398 MET cc_start: 0.8150 (tpp) cc_final: 0.7870 (tpp) REVERT: C 414 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7834 (tp30) REVERT: C 478 MET cc_start: 0.8764 (mmm) cc_final: 0.8323 (mmp) REVERT: C 498 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6883 (mtmm) REVERT: C 591 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7177 (mttt) REVERT: C 601 MET cc_start: 0.8493 (mtm) cc_final: 0.8059 (mtp) REVERT: C 604 LYS cc_start: 0.7526 (mttp) cc_final: 0.7278 (mmmm) REVERT: C 608 GLU cc_start: 0.7451 (tt0) cc_final: 0.7164 (tt0) REVERT: C 631 LYS cc_start: 0.8150 (tttp) cc_final: 0.7939 (tttm) REVERT: C 633 LYS cc_start: 0.8019 (mttt) cc_final: 0.7717 (mttp) REVERT: C 642 GLU cc_start: 0.6055 (tp30) cc_final: 0.5702 (tm-30) REVERT: C 647 SER cc_start: 0.8349 (t) cc_final: 0.7970 (p) REVERT: C 657 MET cc_start: 0.6800 (mmm) cc_final: 0.6530 (tmm) REVERT: C 660 LYS cc_start: 0.7808 (mttt) cc_final: 0.7476 (mtpp) REVERT: C 695 GLU cc_start: 0.6628 (tt0) cc_final: 0.6387 (pm20) REVERT: C 696 LYS cc_start: 0.8038 (mptp) cc_final: 0.7693 (mmtp) REVERT: C 731 ASN cc_start: 0.7557 (t0) cc_final: 0.6984 (m-40) REVERT: C 771 LYS cc_start: 0.8395 (mttp) cc_final: 0.8066 (mttm) REVERT: C 777 ASP cc_start: 0.7622 (t70) cc_final: 0.7386 (t0) REVERT: C 783 MET cc_start: 0.7325 (mmm) cc_final: 0.7044 (mmm) REVERT: C 831 THR cc_start: 0.8826 (m) cc_final: 0.8379 (p) REVERT: C 880 PHE cc_start: 0.7419 (m-80) cc_final: 0.6637 (t80) REVERT: C 887 LEU cc_start: 0.7858 (tt) cc_final: 0.7605 (tp) REVERT: C 944 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7949 (mp) REVERT: C 963 GLU cc_start: 0.6920 (tt0) cc_final: 0.6528 (tt0) REVERT: C 977 HIS cc_start: 0.6944 (t-90) cc_final: 0.6509 (t-170) REVERT: C 1041 ARG cc_start: 0.7593 (mmt90) cc_final: 0.6637 (mmt90) outliers start: 68 outliers final: 24 residues processed: 759 average time/residue: 2.0724 time to fit residues: 1913.7767 Evaluate side-chains 654 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 615 time to evaluate : 4.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 944 ILE Chi-restraints excluded: chain C residue 949 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 159 optimal weight: 0.0070 chunk 126 optimal weight: 0.0060 chunk 244 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN B 112 GLN B 241 GLN B 720 ASN B 722 GLN B 829 GLN B 977 HIS C 108 GLN C 112 GLN C 415 ASN C 727 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24697 Z= 0.165 Angle : 0.549 6.016 33522 Z= 0.294 Chirality : 0.040 0.158 3918 Planarity : 0.005 0.055 4275 Dihedral : 9.450 106.449 3668 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.78 % Allowed : 16.64 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.15), residues: 3136 helix: 1.93 (0.13), residues: 1659 sheet: 0.25 (0.24), residues: 434 loop : -0.44 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 635 HIS 0.002 0.001 HIS B 500 PHE 0.015 0.001 PHE A 459 TYR 0.015 0.001 TYR C 664 ARG 0.004 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 636 time to evaluate : 4.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6314 (ttt) cc_final: 0.5894 (tpp) REVERT: A 34 GLN cc_start: 0.7180 (tt0) cc_final: 0.6944 (tt0) REVERT: A 87 GLN cc_start: 0.8257 (mt0) cc_final: 0.7903 (mt0) REVERT: A 95 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6445 (mt-10) REVERT: A 101 ASP cc_start: 0.7925 (m-30) cc_final: 0.7680 (m-30) REVERT: A 112 GLN cc_start: 0.8122 (tt0) cc_final: 0.7704 (mt0) REVERT: A 155 LYS cc_start: 0.8274 (mttt) cc_final: 0.7790 (mtmm) REVERT: A 193 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7864 (mt) REVERT: A 201 SER cc_start: 0.7730 (m) cc_final: 0.7514 (m) REVERT: A 261 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7337 (mtt90) REVERT: A 284 LYS cc_start: 0.7278 (mttt) cc_final: 0.6885 (mmmm) REVERT: A 334 ARG cc_start: 0.6191 (tpp-160) cc_final: 0.5792 (ttm110) REVERT: A 338 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6565 (mt-10) REVERT: A 342 HIS cc_start: 0.5752 (t70) cc_final: 0.5164 (m-70) REVERT: A 346 GLU cc_start: 0.6576 (mt-10) cc_final: 0.5962 (mt-10) REVERT: A 349 ILE cc_start: 0.6952 (mm) cc_final: 0.6359 (mt) REVERT: A 353 ILE cc_start: 0.6909 (mm) cc_final: 0.6646 (mt) REVERT: A 390 ILE cc_start: 0.7580 (mt) cc_final: 0.7271 (mm) REVERT: A 407 ASP cc_start: 0.6774 (m-30) cc_final: 0.6532 (m-30) REVERT: A 408 ASP cc_start: 0.6522 (m-30) cc_final: 0.6196 (m-30) REVERT: A 410 ILE cc_start: 0.6288 (mm) cc_final: 0.5852 (mt) REVERT: A 429 THR cc_start: 0.7669 (m) cc_final: 0.7347 (t) REVERT: A 452 VAL cc_start: 0.8018 (t) cc_final: 0.7742 (m) REVERT: A 478 MET cc_start: 0.5998 (mmp) cc_final: 0.5664 (mpm) REVERT: A 585 THR cc_start: 0.8488 (m) cc_final: 0.8279 (p) REVERT: A 605 ASP cc_start: 0.6912 (p0) cc_final: 0.6611 (m-30) REVERT: A 608 GLU cc_start: 0.6700 (tt0) cc_final: 0.6474 (tm-30) REVERT: A 642 GLU cc_start: 0.6510 (mt-10) cc_final: 0.5961 (mp0) REVERT: A 647 SER cc_start: 0.7335 (OUTLIER) cc_final: 0.7057 (p) REVERT: A 653 MET cc_start: 0.6385 (mtp) cc_final: 0.5991 (mmt) REVERT: A 704 ILE cc_start: 0.7163 (mt) cc_final: 0.6934 (mm) REVERT: A 752 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7636 (ttp80) REVERT: A 766 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7561 (mtm-85) REVERT: A 842 MET cc_start: 0.6053 (mtm) cc_final: 0.5537 (mtm) REVERT: A 862 TYR cc_start: 0.7137 (p90) cc_final: 0.6911 (p90) REVERT: A 892 CYS cc_start: 0.7163 (m) cc_final: 0.6746 (m) REVERT: A 949 LEU cc_start: 0.7684 (tp) cc_final: 0.7354 (tm) REVERT: A 952 LYS cc_start: 0.6738 (tttt) cc_final: 0.6213 (ttpp) REVERT: A 960 PHE cc_start: 0.6550 (t80) cc_final: 0.5784 (t80) REVERT: A 984 ARG cc_start: 0.6171 (ttt90) cc_final: 0.5103 (ttt90) REVERT: A 1018 VAL cc_start: 0.7035 (OUTLIER) cc_final: 0.6795 (t) REVERT: A 1022 VAL cc_start: 0.7278 (p) cc_final: 0.7020 (m) REVERT: B 20 MET cc_start: 0.6157 (mtt) cc_final: 0.5819 (tpp) REVERT: B 164 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6432 (mt-10) REVERT: B 229 VAL cc_start: 0.7932 (p) cc_final: 0.7693 (m) REVERT: B 237 GLN cc_start: 0.7267 (tp40) cc_final: 0.6895 (tm130) REVERT: B 304 GLU cc_start: 0.6407 (mt-10) cc_final: 0.6130 (mt-10) REVERT: B 312 GLU cc_start: 0.6417 (mt-10) cc_final: 0.6206 (mt-10) REVERT: B 356 PHE cc_start: 0.7758 (t80) cc_final: 0.7492 (t80) REVERT: B 363 ARG cc_start: 0.7186 (mtp85) cc_final: 0.6945 (mtt180) REVERT: B 366 ILE cc_start: 0.8119 (tt) cc_final: 0.7733 (tp) REVERT: B 407 ASP cc_start: 0.7323 (t0) cc_final: 0.7107 (t0) REVERT: B 439 SER cc_start: 0.8129 (m) cc_final: 0.7911 (p) REVERT: B 456 MET cc_start: 0.7920 (ptm) cc_final: 0.7506 (ttp) REVERT: B 478 MET cc_start: 0.7941 (mmp) cc_final: 0.7364 (mmp) REVERT: B 487 THR cc_start: 0.8563 (m) cc_final: 0.7898 (p) REVERT: B 518 PHE cc_start: 0.7332 (t80) cc_final: 0.7043 (t80) REVERT: B 530 GLN cc_start: 0.6484 (mt0) cc_final: 0.6010 (mt0) REVERT: B 536 MET cc_start: 0.6276 (ttm) cc_final: 0.6026 (ttt) REVERT: B 692 GLN cc_start: 0.7331 (mt0) cc_final: 0.7034 (mt0) REVERT: B 718 ARG cc_start: 0.6101 (ptt90) cc_final: 0.5808 (pmm-80) REVERT: B 768 ARG cc_start: 0.6097 (mtp85) cc_final: 0.5798 (ttp80) REVERT: B 786 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: B 798 GLU cc_start: 0.7021 (mp0) cc_final: 0.6623 (mp0) REVERT: B 846 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7013 (mt-10) REVERT: B 862 TYR cc_start: 0.7816 (p90) cc_final: 0.7496 (p90) REVERT: B 880 PHE cc_start: 0.7551 (t80) cc_final: 0.7279 (t80) REVERT: B 882 TYR cc_start: 0.7134 (m-80) cc_final: 0.6821 (m-80) REVERT: B 887 LEU cc_start: 0.8103 (tp) cc_final: 0.7654 (tm) REVERT: B 964 LEU cc_start: 0.8090 (mt) cc_final: 0.7833 (mp) REVERT: B 972 LEU cc_start: 0.7616 (mp) cc_final: 0.7338 (mt) REVERT: B 987 ILE cc_start: 0.8025 (mt) cc_final: 0.7753 (mm) REVERT: B 997 VAL cc_start: 0.8220 (p) cc_final: 0.7859 (m) REVERT: B 1023 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7180 (mm) REVERT: B 1045 LYS cc_start: 0.6936 (mmmt) cc_final: 0.6663 (mttm) REVERT: C 11 PHE cc_start: 0.8448 (t80) cc_final: 0.8001 (t80) REVERT: C 20 MET cc_start: 0.8134 (mtp) cc_final: 0.7774 (mtp) REVERT: C 66 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6589 (mt-10) REVERT: C 67 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: C 124 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6843 (mtt-85) REVERT: C 188 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8277 (mt) REVERT: C 192 LYS cc_start: 0.7577 (mttt) cc_final: 0.6760 (mtmt) REVERT: C 196 TYR cc_start: 0.8411 (m-80) cc_final: 0.7794 (m-80) REVERT: C 197 GLN cc_start: 0.7703 (mp10) cc_final: 0.7152 (mp10) REVERT: C 261 ARG cc_start: 0.7733 (mtt-85) cc_final: 0.7127 (mmm160) REVERT: C 314 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7029 (mtm110) REVERT: C 329 THR cc_start: 0.8153 (m) cc_final: 0.7804 (p) REVERT: C 346 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6687 (mt-10) REVERT: C 370 LEU cc_start: 0.8468 (mt) cc_final: 0.8199 (mp) REVERT: C 398 MET cc_start: 0.8234 (tpp) cc_final: 0.7964 (tpp) REVERT: C 414 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: C 420 MET cc_start: 0.8198 (mtp) cc_final: 0.7736 (mtt) REVERT: C 436 GLN cc_start: 0.6882 (tp40) cc_final: 0.6339 (tp-100) REVERT: C 445 ILE cc_start: 0.8188 (mt) cc_final: 0.7881 (mm) REVERT: C 478 MET cc_start: 0.8534 (mmm) cc_final: 0.8065 (mmp) REVERT: C 591 LYS cc_start: 0.7512 (mtpt) cc_final: 0.7046 (mttt) REVERT: C 594 ASP cc_start: 0.6444 (t70) cc_final: 0.6175 (t70) REVERT: C 601 MET cc_start: 0.8451 (mtm) cc_final: 0.8039 (mtp) REVERT: C 602 ASN cc_start: 0.7180 (OUTLIER) cc_final: 0.6512 (m-40) REVERT: C 603 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6425 (mm-30) REVERT: C 604 LYS cc_start: 0.7393 (mttp) cc_final: 0.7185 (mmmm) REVERT: C 608 GLU cc_start: 0.7369 (tt0) cc_final: 0.7044 (tt0) REVERT: C 633 LYS cc_start: 0.7836 (mttt) cc_final: 0.7564 (mttm) REVERT: C 643 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7835 (t) REVERT: C 653 MET cc_start: 0.8348 (tpt) cc_final: 0.8108 (mmm) REVERT: C 657 MET cc_start: 0.6747 (mmm) cc_final: 0.6478 (tmm) REVERT: C 695 GLU cc_start: 0.6589 (tt0) cc_final: 0.6377 (pm20) REVERT: C 696 LYS cc_start: 0.7959 (mptp) cc_final: 0.7605 (mmtp) REVERT: C 724 ASP cc_start: 0.7512 (m-30) cc_final: 0.7279 (m-30) REVERT: C 731 ASN cc_start: 0.7545 (t0) cc_final: 0.6992 (m-40) REVERT: C 771 LYS cc_start: 0.8314 (mttp) cc_final: 0.8014 (mttm) REVERT: C 783 MET cc_start: 0.7297 (mmm) cc_final: 0.7040 (mmm) REVERT: C 880 PHE cc_start: 0.7344 (m-80) cc_final: 0.6634 (t80) REVERT: C 887 LEU cc_start: 0.7825 (tt) cc_final: 0.7597 (tp) REVERT: C 955 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8282 (mm) REVERT: C 963 GLU cc_start: 0.6972 (tt0) cc_final: 0.6564 (tt0) REVERT: C 977 HIS cc_start: 0.6932 (t-90) cc_final: 0.6460 (t-170) REVERT: C 988 MET cc_start: 0.7556 (ptp) cc_final: 0.7232 (ptp) outliers start: 72 outliers final: 34 residues processed: 675 average time/residue: 2.1602 time to fit residues: 1775.9145 Evaluate side-chains 647 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 600 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 955 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 235 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 283 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 281 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A 953 ASN A1011 GLN B 91 GLN B 112 GLN B 241 GLN ** B 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 HIS C 104 GLN C 298 ASN C 415 ASN C 530 GLN C 598 ASN C 727 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24697 Z= 0.349 Angle : 0.603 6.197 33522 Z= 0.325 Chirality : 0.043 0.172 3918 Planarity : 0.005 0.056 4275 Dihedral : 8.917 88.007 3633 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.82 % Allowed : 17.53 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.15), residues: 3136 helix: 1.70 (0.12), residues: 1671 sheet: 0.24 (0.24), residues: 438 loop : -0.58 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 790 HIS 0.006 0.001 HIS B 694 PHE 0.018 0.002 PHE A 459 TYR 0.020 0.002 TYR C 820 ARG 0.005 0.001 ARG C 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 605 time to evaluate : 3.642 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 1 MET cc_start: 0.6262 (ttt) cc_final: 0.5831 (tpp) REVERT: A 18 VAL cc_start: 0.7775 (t) cc_final: 0.7532 (m) REVERT: A 34 GLN cc_start: 0.7167 (tt0) cc_final: 0.6736 (tt0) REVERT: A 87 GLN cc_start: 0.8306 (mt0) cc_final: 0.8025 (mt0) REVERT: A 95 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6513 (mt-10) REVERT: A 101 ASP cc_start: 0.8090 (m-30) cc_final: 0.7825 (m-30) REVERT: A 112 GLN cc_start: 0.8175 (tt0) cc_final: 0.7766 (mt0) REVERT: A 155 LYS cc_start: 0.8272 (mttt) cc_final: 0.7811 (mtmm) REVERT: A 193 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7864 (mt) REVERT: A 284 LYS cc_start: 0.7402 (mttt) cc_final: 0.6929 (mmmm) REVERT: A 312 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6223 (mm-30) REVERT: A 315 LYS cc_start: 0.7407 (mttt) cc_final: 0.6909 (mttt) REVERT: A 334 ARG cc_start: 0.6240 (tpp-160) cc_final: 0.5912 (ttm110) REVERT: A 338 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6686 (mt-10) REVERT: A 342 HIS cc_start: 0.5740 (t70) cc_final: 0.5119 (m-70) REVERT: A 346 GLU cc_start: 0.6608 (mt-10) cc_final: 0.5976 (mt-10) REVERT: A 349 ILE cc_start: 0.6942 (mm) cc_final: 0.6360 (mt) REVERT: A 353 ILE cc_start: 0.6885 (mm) cc_final: 0.6619 (mt) REVERT: A 390 ILE cc_start: 0.7610 (mt) cc_final: 0.7336 (mm) REVERT: A 410 ILE cc_start: 0.6199 (mm) cc_final: 0.5952 (mt) REVERT: A 429 THR cc_start: 0.7607 (m) cc_final: 0.7265 (t) REVERT: A 452 VAL cc_start: 0.8043 (t) cc_final: 0.7765 (m) REVERT: A 478 MET cc_start: 0.6159 (mmp) cc_final: 0.5726 (mpm) REVERT: A 605 ASP cc_start: 0.6948 (p0) cc_final: 0.6561 (m-30) REVERT: A 608 GLU cc_start: 0.6745 (tt0) cc_final: 0.6543 (tm-30) REVERT: A 647 SER cc_start: 0.7364 (OUTLIER) cc_final: 0.7011 (p) REVERT: A 653 MET cc_start: 0.6352 (mtp) cc_final: 0.5907 (mmt) REVERT: A 666 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6580 (ttp) REVERT: A 707 LEU cc_start: 0.5821 (mt) cc_final: 0.5559 (mm) REVERT: A 809 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6851 (pt0) REVERT: A 842 MET cc_start: 0.6187 (mtm) cc_final: 0.5668 (mtm) REVERT: A 862 TYR cc_start: 0.7161 (p90) cc_final: 0.6865 (p90) REVERT: A 892 CYS cc_start: 0.7038 (m) cc_final: 0.6619 (m) REVERT: A 898 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7173 (tp30) REVERT: A 949 LEU cc_start: 0.7630 (tp) cc_final: 0.7319 (tm) REVERT: A 952 LYS cc_start: 0.7025 (tttt) cc_final: 0.6458 (ttpp) REVERT: A 960 PHE cc_start: 0.6494 (t80) cc_final: 0.5747 (t80) REVERT: A 984 ARG cc_start: 0.6138 (ttt90) cc_final: 0.5045 (ttt90) REVERT: A 1022 VAL cc_start: 0.7394 (p) cc_final: 0.7045 (m) REVERT: B 20 MET cc_start: 0.6183 (mtt) cc_final: 0.5834 (tpp) REVERT: B 55 GLU cc_start: 0.7496 (tt0) cc_final: 0.6807 (mp0) REVERT: B 229 VAL cc_start: 0.8033 (p) cc_final: 0.7782 (m) REVERT: B 237 GLN cc_start: 0.7260 (tp40) cc_final: 0.6862 (tm130) REVERT: B 304 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6105 (mt-10) REVERT: B 335 LEU cc_start: 0.6801 (mt) cc_final: 0.6542 (mp) REVERT: B 359 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5814 (mt) REVERT: B 363 ARG cc_start: 0.7233 (mtp85) cc_final: 0.6964 (mtt180) REVERT: B 366 ILE cc_start: 0.8262 (tt) cc_final: 0.7920 (tp) REVERT: B 407 ASP cc_start: 0.7515 (t0) cc_final: 0.7039 (t0) REVERT: B 522 PHE cc_start: 0.7623 (t80) cc_final: 0.7360 (t80) REVERT: B 530 GLN cc_start: 0.6548 (mt0) cc_final: 0.6079 (mt0) REVERT: B 536 MET cc_start: 0.6290 (ttm) cc_final: 0.6024 (ttt) REVERT: B 692 GLN cc_start: 0.7388 (mt0) cc_final: 0.7162 (mt0) REVERT: B 695 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.6091 (mm-30) REVERT: B 718 ARG cc_start: 0.5978 (ptt90) cc_final: 0.5678 (pmm-80) REVERT: B 749 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.7269 (t0) REVERT: B 768 ARG cc_start: 0.6187 (mtp85) cc_final: 0.5840 (ttp80) REVERT: B 786 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: B 798 GLU cc_start: 0.7043 (mp0) cc_final: 0.6731 (mp0) REVERT: B 807 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7610 (t) REVERT: B 880 PHE cc_start: 0.7409 (t80) cc_final: 0.7192 (t80) REVERT: B 882 TYR cc_start: 0.7177 (m-80) cc_final: 0.6658 (m-80) REVERT: B 887 LEU cc_start: 0.8181 (tp) cc_final: 0.7742 (tm) REVERT: B 964 LEU cc_start: 0.8138 (mt) cc_final: 0.7884 (mp) REVERT: B 987 ILE cc_start: 0.8089 (mt) cc_final: 0.7836 (mm) REVERT: B 997 VAL cc_start: 0.8250 (p) cc_final: 0.7913 (m) REVERT: B 1045 LYS cc_start: 0.6792 (mmmt) cc_final: 0.6347 (ttmm) REVERT: C 20 MET cc_start: 0.8108 (mtp) cc_final: 0.7759 (mtp) REVERT: C 66 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6479 (mt-10) REVERT: C 67 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: C 124 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.6997 (mtt-85) REVERT: C 188 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8320 (mt) REVERT: C 192 LYS cc_start: 0.7664 (mttt) cc_final: 0.6938 (mtpt) REVERT: C 196 TYR cc_start: 0.8425 (m-80) cc_final: 0.7812 (m-80) REVERT: C 197 GLN cc_start: 0.7667 (mp10) cc_final: 0.7035 (mp-120) REVERT: C 242 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8405 (p) REVERT: C 261 ARG cc_start: 0.7742 (mtt-85) cc_final: 0.7058 (mmm160) REVERT: C 284 LYS cc_start: 0.7747 (mmtm) cc_final: 0.7542 (mmtp) REVERT: C 293 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7838 (mt) REVERT: C 314 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7090 (mtm110) REVERT: C 329 THR cc_start: 0.8197 (m) cc_final: 0.7788 (p) REVERT: C 346 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6744 (mt-10) REVERT: C 365 THR cc_start: 0.7707 (t) cc_final: 0.7293 (m) REVERT: C 370 LEU cc_start: 0.8482 (mt) cc_final: 0.8166 (mp) REVERT: C 398 MET cc_start: 0.8275 (tpp) cc_final: 0.8025 (tpp) REVERT: C 414 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6886 (tp30) REVERT: C 436 GLN cc_start: 0.6972 (tp40) cc_final: 0.6722 (tp-100) REVERT: C 445 ILE cc_start: 0.8290 (mt) cc_final: 0.7962 (mm) REVERT: C 478 MET cc_start: 0.8553 (mmm) cc_final: 0.8070 (mmp) REVERT: C 591 LYS cc_start: 0.7587 (mtpt) cc_final: 0.7115 (mttt) REVERT: C 601 MET cc_start: 0.8488 (mtm) cc_final: 0.8074 (mtp) REVERT: C 603 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6353 (mm-30) REVERT: C 633 LYS cc_start: 0.7888 (mttt) cc_final: 0.7680 (mttp) REVERT: C 643 THR cc_start: 0.8228 (p) cc_final: 0.7843 (t) REVERT: C 657 MET cc_start: 0.6759 (mmm) cc_final: 0.6480 (tmm) REVERT: C 695 GLU cc_start: 0.6610 (tt0) cc_final: 0.6366 (pm20) REVERT: C 696 LYS cc_start: 0.8022 (mptp) cc_final: 0.7696 (mmtp) REVERT: C 731 ASN cc_start: 0.7570 (t0) cc_final: 0.6987 (m-40) REVERT: C 771 LYS cc_start: 0.8296 (mttp) cc_final: 0.7985 (mttm) REVERT: C 783 MET cc_start: 0.7329 (mmm) cc_final: 0.7038 (mmm) REVERT: C 880 PHE cc_start: 0.7419 (m-80) cc_final: 0.6650 (t80) REVERT: C 887 LEU cc_start: 0.7867 (tt) cc_final: 0.7642 (tp) REVERT: C 896 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7674 (mt) REVERT: C 955 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8389 (mm) REVERT: C 963 GLU cc_start: 0.7059 (tt0) cc_final: 0.6620 (tt0) REVERT: C 977 HIS cc_start: 0.6935 (t-90) cc_final: 0.6454 (t-170) outliers start: 99 outliers final: 55 residues processed: 657 average time/residue: 2.1483 time to fit residues: 1717.7237 Evaluate side-chains 663 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 589 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 724 ASP Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 749 ASN Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 963 GLU Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 949 LEU Chi-restraints excluded: chain C residue 955 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 301 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN A 935 ASN A 953 ASN A1011 GLN B 241 GLN B 722 GLN B 977 HIS C 415 ASN C 530 GLN C 598 ASN C 727 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24697 Z= 0.246 Angle : 0.546 6.058 33522 Z= 0.290 Chirality : 0.041 0.153 3918 Planarity : 0.004 0.053 4275 Dihedral : 8.361 85.517 3622 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.75 % Allowed : 18.34 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.15), residues: 3136 helix: 1.92 (0.13), residues: 1667 sheet: 0.24 (0.24), residues: 438 loop : -0.53 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 790 HIS 0.004 0.001 HIS B 694 PHE 0.017 0.001 PHE A 459 TYR 0.014 0.001 TYR C 820 ARG 0.005 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 605 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6292 (ttt) cc_final: 0.5855 (tpp) REVERT: A 34 GLN cc_start: 0.7244 (tt0) cc_final: 0.6875 (tt0) REVERT: A 95 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6464 (mt-10) REVERT: A 101 ASP cc_start: 0.7976 (m-30) cc_final: 0.7739 (m-30) REVERT: A 112 GLN cc_start: 0.8164 (tt0) cc_final: 0.7745 (mt0) REVERT: A 155 LYS cc_start: 0.8243 (mttt) cc_final: 0.7787 (mtmm) REVERT: A 193 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7853 (mt) REVERT: A 284 LYS cc_start: 0.7343 (mttt) cc_final: 0.6922 (mmmm) REVERT: A 312 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6188 (mm-30) REVERT: A 315 LYS cc_start: 0.7381 (mttt) cc_final: 0.6969 (mttp) REVERT: A 338 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6760 (mt-10) REVERT: A 342 HIS cc_start: 0.5757 (t70) cc_final: 0.5136 (m-70) REVERT: A 346 GLU cc_start: 0.6577 (mt-10) cc_final: 0.5953 (mt-10) REVERT: A 349 ILE cc_start: 0.6788 (mm) cc_final: 0.6203 (mt) REVERT: A 353 ILE cc_start: 0.6873 (mm) cc_final: 0.6601 (mt) REVERT: A 390 ILE cc_start: 0.7569 (mt) cc_final: 0.7335 (mm) REVERT: A 410 ILE cc_start: 0.6179 (mm) cc_final: 0.5933 (mt) REVERT: A 429 THR cc_start: 0.7586 (m) cc_final: 0.7207 (t) REVERT: A 435 MET cc_start: 0.7107 (tpp) cc_final: 0.6874 (tpp) REVERT: A 468 ARG cc_start: 0.6752 (mtm-85) cc_final: 0.6197 (ttm-80) REVERT: A 478 MET cc_start: 0.6139 (mmp) cc_final: 0.5715 (mpm) REVERT: A 605 ASP cc_start: 0.6917 (p0) cc_final: 0.6516 (m-30) REVERT: A 608 GLU cc_start: 0.6833 (tt0) cc_final: 0.6574 (tm-30) REVERT: A 647 SER cc_start: 0.7268 (t) cc_final: 0.6976 (p) REVERT: A 653 MET cc_start: 0.6349 (mtp) cc_final: 0.5958 (mmt) REVERT: A 666 MET cc_start: 0.6975 (mtm) cc_final: 0.6544 (ttp) REVERT: A 707 LEU cc_start: 0.5893 (mt) cc_final: 0.5664 (mm) REVERT: A 736 GLN cc_start: 0.6552 (mt0) cc_final: 0.6315 (mt0) REVERT: A 752 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7640 (ttp80) REVERT: A 809 GLU cc_start: 0.7131 (pt0) cc_final: 0.6908 (pt0) REVERT: A 862 TYR cc_start: 0.7153 (p90) cc_final: 0.6879 (p90) REVERT: A 892 CYS cc_start: 0.7139 (m) cc_final: 0.6702 (m) REVERT: A 898 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7120 (tp30) REVERT: A 949 LEU cc_start: 0.7595 (tp) cc_final: 0.7290 (tm) REVERT: A 952 LYS cc_start: 0.7074 (tttt) cc_final: 0.6550 (ttpp) REVERT: A 960 PHE cc_start: 0.6482 (t80) cc_final: 0.5793 (t80) REVERT: A 984 ARG cc_start: 0.6144 (ttt90) cc_final: 0.5038 (ttt90) REVERT: A 1022 VAL cc_start: 0.7376 (p) cc_final: 0.7025 (m) REVERT: B 1 MET cc_start: 0.4060 (ttm) cc_final: 0.3828 (ttt) REVERT: B 20 MET cc_start: 0.6141 (mtt) cc_final: 0.5849 (tpp) REVERT: B 55 GLU cc_start: 0.7510 (tt0) cc_final: 0.6872 (mp0) REVERT: B 229 VAL cc_start: 0.8006 (p) cc_final: 0.7757 (m) REVERT: B 237 GLN cc_start: 0.7269 (tp40) cc_final: 0.6886 (tm130) REVERT: B 304 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.6092 (mt-10) REVERT: B 356 PHE cc_start: 0.7747 (t80) cc_final: 0.7475 (t80) REVERT: B 359 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5635 (mt) REVERT: B 363 ARG cc_start: 0.7237 (mtp85) cc_final: 0.6975 (mtt180) REVERT: B 366 ILE cc_start: 0.8214 (tt) cc_final: 0.7850 (tp) REVERT: B 407 ASP cc_start: 0.7451 (t0) cc_final: 0.7246 (t0) REVERT: B 420 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8194 (mtm) REVERT: B 522 PHE cc_start: 0.7656 (t80) cc_final: 0.7404 (t80) REVERT: B 530 GLN cc_start: 0.6536 (mt0) cc_final: 0.6039 (mt0) REVERT: B 536 MET cc_start: 0.6289 (ttm) cc_final: 0.6027 (ttt) REVERT: B 690 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.6810 (p) REVERT: B 718 ARG cc_start: 0.6008 (ptt90) cc_final: 0.5701 (pmm-80) REVERT: B 749 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7197 (t0) REVERT: B 768 ARG cc_start: 0.6180 (mtp85) cc_final: 0.5840 (ttp80) REVERT: B 786 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: B 798 GLU cc_start: 0.7032 (mp0) cc_final: 0.6696 (mp0) REVERT: B 807 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7619 (t) REVERT: B 880 PHE cc_start: 0.7533 (t80) cc_final: 0.7275 (t80) REVERT: B 882 TYR cc_start: 0.7068 (m-80) cc_final: 0.6739 (m-80) REVERT: B 887 LEU cc_start: 0.8184 (tp) cc_final: 0.7753 (tm) REVERT: B 964 LEU cc_start: 0.8091 (mt) cc_final: 0.7835 (mp) REVERT: B 972 LEU cc_start: 0.7654 (mp) cc_final: 0.7381 (mt) REVERT: B 987 ILE cc_start: 0.8108 (mt) cc_final: 0.7854 (mm) REVERT: B 997 VAL cc_start: 0.8281 (p) cc_final: 0.7961 (m) REVERT: B 1045 LYS cc_start: 0.6779 (mmmt) cc_final: 0.6435 (mttm) REVERT: C 8 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7454 (mtt-85) REVERT: C 11 PHE cc_start: 0.8487 (t80) cc_final: 0.8059 (t80) REVERT: C 20 MET cc_start: 0.8079 (mtp) cc_final: 0.7749 (mtp) REVERT: C 66 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6473 (mt-10) REVERT: C 67 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: C 124 ARG cc_start: 0.7232 (mtm-85) cc_final: 0.6999 (mtt-85) REVERT: C 192 LYS cc_start: 0.7644 (mttt) cc_final: 0.6917 (mtpt) REVERT: C 196 TYR cc_start: 0.8408 (m-80) cc_final: 0.7774 (m-80) REVERT: C 197 GLN cc_start: 0.7731 (mp10) cc_final: 0.7084 (mp-120) REVERT: C 242 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8387 (p) REVERT: C 259 GLU cc_start: 0.7603 (pt0) cc_final: 0.7212 (pt0) REVERT: C 261 ARG cc_start: 0.7689 (mtt-85) cc_final: 0.7153 (mmm160) REVERT: C 314 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7115 (mtm110) REVERT: C 329 THR cc_start: 0.8185 (m) cc_final: 0.7837 (p) REVERT: C 346 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6686 (mt-10) REVERT: C 365 THR cc_start: 0.7601 (t) cc_final: 0.7287 (m) REVERT: C 370 LEU cc_start: 0.8497 (mt) cc_final: 0.8187 (mp) REVERT: C 398 MET cc_start: 0.8241 (tpp) cc_final: 0.7965 (tpp) REVERT: C 420 MET cc_start: 0.8201 (mtp) cc_final: 0.7844 (mtt) REVERT: C 445 ILE cc_start: 0.8240 (mt) cc_final: 0.7921 (mm) REVERT: C 478 MET cc_start: 0.8535 (mmm) cc_final: 0.8061 (mmp) REVERT: C 591 LYS cc_start: 0.7525 (mtpt) cc_final: 0.7083 (mttt) REVERT: C 601 MET cc_start: 0.8493 (mtm) cc_final: 0.7977 (mtp) REVERT: C 627 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8585 (tt) REVERT: C 657 MET cc_start: 0.6764 (mmm) cc_final: 0.6504 (tmm) REVERT: C 695 GLU cc_start: 0.6669 (tt0) cc_final: 0.6393 (pm20) REVERT: C 696 LYS cc_start: 0.7982 (mptp) cc_final: 0.7677 (mmtp) REVERT: C 731 ASN cc_start: 0.7574 (t0) cc_final: 0.7025 (m-40) REVERT: C 771 LYS cc_start: 0.8288 (mttp) cc_final: 0.7970 (mttm) REVERT: C 783 MET cc_start: 0.7301 (mmm) cc_final: 0.7026 (mmm) REVERT: C 880 PHE cc_start: 0.7411 (m-80) cc_final: 0.6650 (t80) REVERT: C 887 LEU cc_start: 0.7840 (tt) cc_final: 0.7621 (tp) REVERT: C 949 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8153 (tp) REVERT: C 955 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8319 (mm) REVERT: C 963 GLU cc_start: 0.6959 (tt0) cc_final: 0.6607 (tt0) REVERT: C 969 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6479 (mt-10) REVERT: C 977 HIS cc_start: 0.6981 (t-90) cc_final: 0.6523 (t-170) outliers start: 97 outliers final: 52 residues processed: 656 average time/residue: 2.2056 time to fit residues: 1765.5903 Evaluate side-chains 662 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 595 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 724 ASP Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 749 ASN Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 963 GLU Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 949 LEU Chi-restraints excluded: chain C residue 955 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A 953 ASN A1011 GLN B 104 GLN B 112 GLN B 241 GLN B 722 GLN B 977 HIS C 415 ASN C 530 GLN C 598 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24697 Z= 0.262 Angle : 0.550 6.044 33522 Z= 0.292 Chirality : 0.041 0.152 3918 Planarity : 0.004 0.052 4275 Dihedral : 8.111 79.099 3617 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.05 % Allowed : 18.42 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.15), residues: 3136 helix: 1.94 (0.13), residues: 1668 sheet: 0.24 (0.24), residues: 438 loop : -0.52 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 790 HIS 0.004 0.001 HIS B 694 PHE 0.016 0.001 PHE A 459 TYR 0.015 0.002 TYR C 820 ARG 0.005 0.000 ARG C 535 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 599 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6100 (ttt) cc_final: 0.5698 (tpp) REVERT: A 18 VAL cc_start: 0.7810 (t) cc_final: 0.7593 (m) REVERT: A 34 GLN cc_start: 0.7130 (tt0) cc_final: 0.6757 (tt0) REVERT: A 95 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6427 (mt-10) REVERT: A 101 ASP cc_start: 0.8067 (m-30) cc_final: 0.7823 (m-30) REVERT: A 112 GLN cc_start: 0.8057 (tt0) cc_final: 0.7670 (mt0) REVERT: A 155 LYS cc_start: 0.8263 (mttt) cc_final: 0.7795 (mtmm) REVERT: A 193 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7874 (mt) REVERT: A 284 LYS cc_start: 0.7379 (mttt) cc_final: 0.6969 (mmmm) REVERT: A 312 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6180 (mm-30) REVERT: A 315 LYS cc_start: 0.7418 (mttt) cc_final: 0.7002 (mttp) REVERT: A 338 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6777 (mt-10) REVERT: A 342 HIS cc_start: 0.5764 (t70) cc_final: 0.5132 (m-70) REVERT: A 346 GLU cc_start: 0.6574 (mt-10) cc_final: 0.5953 (mt-10) REVERT: A 349 ILE cc_start: 0.6788 (mm) cc_final: 0.6190 (mt) REVERT: A 353 ILE cc_start: 0.6877 (mm) cc_final: 0.6594 (mt) REVERT: A 390 ILE cc_start: 0.7529 (mt) cc_final: 0.7293 (mm) REVERT: A 410 ILE cc_start: 0.6204 (mm) cc_final: 0.5938 (mt) REVERT: A 429 THR cc_start: 0.7659 (m) cc_final: 0.7285 (t) REVERT: A 435 MET cc_start: 0.7247 (tpp) cc_final: 0.6948 (tpp) REVERT: A 468 ARG cc_start: 0.6763 (mtm-85) cc_final: 0.6218 (ttm-80) REVERT: A 478 MET cc_start: 0.6104 (mmp) cc_final: 0.5715 (mpm) REVERT: A 605 ASP cc_start: 0.6917 (p0) cc_final: 0.6511 (m-30) REVERT: A 608 GLU cc_start: 0.6789 (tt0) cc_final: 0.6527 (tm-30) REVERT: A 647 SER cc_start: 0.7276 (OUTLIER) cc_final: 0.6992 (p) REVERT: A 653 MET cc_start: 0.6348 (mtp) cc_final: 0.6043 (tpp) REVERT: A 666 MET cc_start: 0.6977 (mtm) cc_final: 0.6540 (ttp) REVERT: A 707 LEU cc_start: 0.5966 (mt) cc_final: 0.5732 (mm) REVERT: A 892 CYS cc_start: 0.7116 (m) cc_final: 0.6668 (m) REVERT: A 898 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7119 (tp30) REVERT: A 949 LEU cc_start: 0.7636 (tp) cc_final: 0.7351 (tm) REVERT: A 952 LYS cc_start: 0.7073 (tttt) cc_final: 0.6553 (ttpp) REVERT: A 960 PHE cc_start: 0.6476 (t80) cc_final: 0.5751 (t80) REVERT: A 1022 VAL cc_start: 0.7397 (p) cc_final: 0.7040 (m) REVERT: B 20 MET cc_start: 0.6138 (mtt) cc_final: 0.5849 (tpp) REVERT: B 55 GLU cc_start: 0.7515 (tt0) cc_final: 0.7258 (tt0) REVERT: B 87 GLN cc_start: 0.8485 (mt0) cc_final: 0.8225 (mt0) REVERT: B 229 VAL cc_start: 0.7986 (p) cc_final: 0.7741 (m) REVERT: B 237 GLN cc_start: 0.7260 (tp40) cc_final: 0.6882 (tm130) REVERT: B 304 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.6085 (mt-10) REVERT: B 335 LEU cc_start: 0.6724 (mt) cc_final: 0.6509 (mp) REVERT: B 359 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5650 (mt) REVERT: B 363 ARG cc_start: 0.7469 (mtp85) cc_final: 0.7229 (mtt180) REVERT: B 366 ILE cc_start: 0.8231 (tt) cc_final: 0.7872 (tp) REVERT: B 522 PHE cc_start: 0.7655 (t80) cc_final: 0.7405 (t80) REVERT: B 530 GLN cc_start: 0.6546 (mt0) cc_final: 0.6037 (mt0) REVERT: B 536 MET cc_start: 0.6260 (ttm) cc_final: 0.6002 (ttt) REVERT: B 575 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.5156 (mpp) REVERT: B 612 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6753 (p) REVERT: B 695 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6085 (mm-30) REVERT: B 718 ARG cc_start: 0.6000 (ptt90) cc_final: 0.5687 (pmm-80) REVERT: B 749 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.7202 (t0) REVERT: B 768 ARG cc_start: 0.6187 (mtp85) cc_final: 0.5839 (ttp80) REVERT: B 786 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: B 798 GLU cc_start: 0.6981 (mp0) cc_final: 0.6638 (mp0) REVERT: B 807 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7618 (t) REVERT: B 880 PHE cc_start: 0.7513 (t80) cc_final: 0.7273 (t80) REVERT: B 882 TYR cc_start: 0.7043 (m-80) cc_final: 0.6722 (m-80) REVERT: B 887 LEU cc_start: 0.8186 (tp) cc_final: 0.7735 (tm) REVERT: B 964 LEU cc_start: 0.8089 (mt) cc_final: 0.7834 (mp) REVERT: B 987 ILE cc_start: 0.8109 (mt) cc_final: 0.7862 (mm) REVERT: B 997 VAL cc_start: 0.8356 (p) cc_final: 0.8048 (m) REVERT: B 1045 LYS cc_start: 0.6762 (mmmt) cc_final: 0.6416 (mttm) REVERT: C 8 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7443 (mtp85) REVERT: C 11 PHE cc_start: 0.8506 (t80) cc_final: 0.8093 (t80) REVERT: C 20 MET cc_start: 0.8100 (mtp) cc_final: 0.7767 (mtp) REVERT: C 66 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6467 (mt-10) REVERT: C 67 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8101 (tm-30) REVERT: C 124 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.7039 (mtt-85) REVERT: C 188 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8346 (mt) REVERT: C 192 LYS cc_start: 0.7647 (mttt) cc_final: 0.6921 (mtpt) REVERT: C 196 TYR cc_start: 0.8397 (m-80) cc_final: 0.7761 (m-80) REVERT: C 197 GLN cc_start: 0.7694 (mp10) cc_final: 0.7038 (mp-120) REVERT: C 242 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8471 (p) REVERT: C 261 ARG cc_start: 0.7694 (mtt-85) cc_final: 0.7165 (mmm160) REVERT: C 329 THR cc_start: 0.8212 (m) cc_final: 0.7842 (p) REVERT: C 346 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6692 (mt-10) REVERT: C 365 THR cc_start: 0.7654 (t) cc_final: 0.7202 (m) REVERT: C 370 LEU cc_start: 0.8488 (mt) cc_final: 0.8138 (mp) REVERT: C 398 MET cc_start: 0.8259 (tpp) cc_final: 0.8010 (tpp) REVERT: C 445 ILE cc_start: 0.8215 (mt) cc_final: 0.7908 (mm) REVERT: C 478 MET cc_start: 0.8539 (mmm) cc_final: 0.8085 (mmp) REVERT: C 591 LYS cc_start: 0.7524 (mtpt) cc_final: 0.7085 (mttt) REVERT: C 601 MET cc_start: 0.8481 (mtm) cc_final: 0.7982 (mtp) REVERT: C 603 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6276 (mm-30) REVERT: C 653 MET cc_start: 0.8361 (tpt) cc_final: 0.7987 (mmm) REVERT: C 657 MET cc_start: 0.6651 (mmm) cc_final: 0.6395 (tmm) REVERT: C 695 GLU cc_start: 0.6623 (tt0) cc_final: 0.6309 (pm20) REVERT: C 696 LYS cc_start: 0.8032 (mptp) cc_final: 0.7687 (mmtp) REVERT: C 731 ASN cc_start: 0.7596 (t0) cc_final: 0.7034 (m-40) REVERT: C 771 LYS cc_start: 0.8289 (mttp) cc_final: 0.7976 (mttm) REVERT: C 783 MET cc_start: 0.7344 (mmm) cc_final: 0.7060 (mmm) REVERT: C 880 PHE cc_start: 0.7413 (m-80) cc_final: 0.6638 (t80) REVERT: C 887 LEU cc_start: 0.7863 (tt) cc_final: 0.7636 (tp) REVERT: C 949 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8154 (tp) REVERT: C 955 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8023 (tp) REVERT: C 963 GLU cc_start: 0.6940 (tt0) cc_final: 0.6582 (tt0) REVERT: C 977 HIS cc_start: 0.6983 (t-90) cc_final: 0.6542 (t-170) outliers start: 105 outliers final: 72 residues processed: 656 average time/residue: 2.1961 time to fit residues: 1743.1138 Evaluate side-chains 673 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 586 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 724 ASP Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 749 ASN Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 963 GLU Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 899 SER Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 949 LEU Chi-restraints excluded: chain C residue 955 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A1011 GLN B 112 GLN B 241 GLN ** B 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 HIS C 415 ASN C 436 GLN C 598 ASN C 727 GLN C 877 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 24697 Z= 0.500 Angle : 0.669 6.372 33522 Z= 0.362 Chirality : 0.046 0.200 3918 Planarity : 0.006 0.055 4275 Dihedral : 8.514 59.343 3610 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.52 % Allowed : 18.73 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3136 helix: 1.39 (0.12), residues: 1672 sheet: 0.08 (0.24), residues: 440 loop : -0.76 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 864 HIS 0.008 0.001 HIS B 694 PHE 0.020 0.002 PHE A 459 TYR 0.021 0.002 TYR C 820 ARG 0.007 0.001 ARG C 535 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 599 time to evaluate : 3.905 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 1 MET cc_start: 0.6054 (ttt) cc_final: 0.5757 (tpp) REVERT: A 18 VAL cc_start: 0.7766 (t) cc_final: 0.7557 (m) REVERT: A 34 GLN cc_start: 0.7221 (tt0) cc_final: 0.6795 (tt0) REVERT: A 95 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6431 (mt-10) REVERT: A 101 ASP cc_start: 0.8150 (m-30) cc_final: 0.7887 (m-30) REVERT: A 112 GLN cc_start: 0.8088 (tt0) cc_final: 0.7696 (mt0) REVERT: A 155 LYS cc_start: 0.8310 (mttt) cc_final: 0.7822 (mtmm) REVERT: A 193 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7840 (mt) REVERT: A 263 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7684 (ptpt) REVERT: A 284 LYS cc_start: 0.7401 (mttt) cc_final: 0.6965 (mmmm) REVERT: A 312 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6221 (mm-30) REVERT: A 315 LYS cc_start: 0.7391 (mttt) cc_final: 0.6996 (mttp) REVERT: A 342 HIS cc_start: 0.5773 (t70) cc_final: 0.5178 (m-70) REVERT: A 346 GLU cc_start: 0.6607 (mt-10) cc_final: 0.6026 (mt-10) REVERT: A 349 ILE cc_start: 0.6930 (mm) cc_final: 0.6347 (mt) REVERT: A 353 ILE cc_start: 0.6912 (mm) cc_final: 0.6633 (mt) REVERT: A 390 ILE cc_start: 0.7549 (mt) cc_final: 0.7312 (mm) REVERT: A 410 ILE cc_start: 0.6269 (mm) cc_final: 0.5982 (mt) REVERT: A 429 THR cc_start: 0.7620 (m) cc_final: 0.7266 (t) REVERT: A 435 MET cc_start: 0.7329 (tpp) cc_final: 0.7052 (tpp) REVERT: A 478 MET cc_start: 0.6149 (mmp) cc_final: 0.5764 (mpm) REVERT: A 608 GLU cc_start: 0.6767 (tt0) cc_final: 0.6506 (tm-30) REVERT: A 647 SER cc_start: 0.7432 (OUTLIER) cc_final: 0.7192 (m) REVERT: A 653 MET cc_start: 0.6318 (mtp) cc_final: 0.6067 (tpp) REVERT: A 666 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6584 (ttp) REVERT: A 707 LEU cc_start: 0.5983 (mt) cc_final: 0.5745 (mm) REVERT: A 892 CYS cc_start: 0.7065 (m) cc_final: 0.6639 (m) REVERT: A 898 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7066 (tp30) REVERT: A 940 GLN cc_start: 0.6936 (mt0) cc_final: 0.6559 (mt0) REVERT: A 949 LEU cc_start: 0.7613 (tp) cc_final: 0.7329 (tm) REVERT: A 952 LYS cc_start: 0.7131 (tttt) cc_final: 0.6608 (ttpp) REVERT: A 960 PHE cc_start: 0.6446 (t80) cc_final: 0.5742 (t80) REVERT: A 1022 VAL cc_start: 0.7361 (p) cc_final: 0.7021 (m) REVERT: B 20 MET cc_start: 0.6165 (mtt) cc_final: 0.5792 (tpp) REVERT: B 55 GLU cc_start: 0.7521 (tt0) cc_final: 0.7274 (tt0) REVERT: B 87 GLN cc_start: 0.8549 (mt0) cc_final: 0.8284 (mt0) REVERT: B 229 VAL cc_start: 0.8041 (p) cc_final: 0.7793 (m) REVERT: B 237 GLN cc_start: 0.7214 (tp40) cc_final: 0.6887 (tm130) REVERT: B 248 ASN cc_start: 0.8471 (m-40) cc_final: 0.8265 (m110) REVERT: B 304 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.6069 (mt-10) REVERT: B 359 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5925 (mt) REVERT: B 363 ARG cc_start: 0.7185 (mtp85) cc_final: 0.6951 (mtt180) REVERT: B 366 ILE cc_start: 0.8333 (tt) cc_final: 0.7980 (tp) REVERT: B 421 SER cc_start: 0.7890 (OUTLIER) cc_final: 0.7525 (m) REVERT: B 522 PHE cc_start: 0.7669 (t80) cc_final: 0.7430 (t80) REVERT: B 530 GLN cc_start: 0.6570 (mt0) cc_final: 0.6032 (mt0) REVERT: B 536 MET cc_start: 0.6233 (ttm) cc_final: 0.5969 (ttt) REVERT: B 575 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5320 (mpp) REVERT: B 695 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.6088 (mm-30) REVERT: B 718 ARG cc_start: 0.5972 (ptt90) cc_final: 0.5658 (pmm-80) REVERT: B 749 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7152 (t0) REVERT: B 768 ARG cc_start: 0.6140 (mtp85) cc_final: 0.5756 (ttp80) REVERT: B 786 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: B 798 GLU cc_start: 0.6987 (mp0) cc_final: 0.6643 (mp0) REVERT: B 807 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7583 (t) REVERT: B 882 TYR cc_start: 0.7142 (m-80) cc_final: 0.6882 (m-80) REVERT: B 887 LEU cc_start: 0.8199 (tp) cc_final: 0.7730 (tm) REVERT: B 964 LEU cc_start: 0.8062 (mt) cc_final: 0.7778 (mp) REVERT: B 987 ILE cc_start: 0.8151 (mt) cc_final: 0.7930 (mm) REVERT: B 997 VAL cc_start: 0.8389 (p) cc_final: 0.8070 (m) REVERT: B 1045 LYS cc_start: 0.6836 (mmmt) cc_final: 0.6499 (mttm) REVERT: C 8 ARG cc_start: 0.7783 (mtp85) cc_final: 0.7499 (mtp85) REVERT: C 20 MET cc_start: 0.8196 (mtp) cc_final: 0.7857 (mtp) REVERT: C 66 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6382 (mt-10) REVERT: C 67 GLN cc_start: 0.8286 (tm-30) cc_final: 0.8086 (tm-30) REVERT: C 124 ARG cc_start: 0.7255 (mtm-85) cc_final: 0.7036 (mtt-85) REVERT: C 188 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8335 (mt) REVERT: C 192 LYS cc_start: 0.7673 (mttt) cc_final: 0.6945 (mtpt) REVERT: C 197 GLN cc_start: 0.7628 (mp10) cc_final: 0.7146 (mp10) REVERT: C 261 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7062 (mmm160) REVERT: C 329 THR cc_start: 0.8365 (m) cc_final: 0.7911 (p) REVERT: C 346 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6771 (mt-10) REVERT: C 365 THR cc_start: 0.7777 (t) cc_final: 0.7367 (m) REVERT: C 370 LEU cc_start: 0.8527 (mt) cc_final: 0.8160 (mm) REVERT: C 398 MET cc_start: 0.8279 (tpp) cc_final: 0.8004 (tpp) REVERT: C 445 ILE cc_start: 0.8265 (mt) cc_final: 0.7923 (mm) REVERT: C 478 MET cc_start: 0.8570 (mmm) cc_final: 0.8131 (mmp) REVERT: C 591 LYS cc_start: 0.7658 (mtpt) cc_final: 0.7219 (mttt) REVERT: C 601 MET cc_start: 0.8531 (mtm) cc_final: 0.8019 (mtp) REVERT: C 602 ASN cc_start: 0.7438 (t0) cc_final: 0.7003 (t0) REVERT: C 657 MET cc_start: 0.6701 (mmm) cc_final: 0.6471 (tmm) REVERT: C 695 GLU cc_start: 0.6618 (tt0) cc_final: 0.6347 (pm20) REVERT: C 696 LYS cc_start: 0.8041 (mptp) cc_final: 0.7690 (mmtp) REVERT: C 731 ASN cc_start: 0.7541 (t0) cc_final: 0.6994 (m-40) REVERT: C 771 LYS cc_start: 0.8338 (mttp) cc_final: 0.8037 (mttm) REVERT: C 783 MET cc_start: 0.7312 (mmm) cc_final: 0.7025 (mmm) REVERT: C 880 PHE cc_start: 0.7459 (m-80) cc_final: 0.6620 (t80) REVERT: C 887 LEU cc_start: 0.7889 (tt) cc_final: 0.7673 (tp) REVERT: C 949 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8181 (tp) REVERT: C 963 GLU cc_start: 0.7061 (tt0) cc_final: 0.6704 (tt0) REVERT: C 977 HIS cc_start: 0.6975 (t-90) cc_final: 0.6529 (t-170) outliers start: 117 outliers final: 77 residues processed: 665 average time/residue: 2.1347 time to fit residues: 1738.7652 Evaluate side-chains 686 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 594 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 724 ASP Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 749 ASN Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 902 ILE Chi-restraints excluded: chain B residue 963 GLU Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain C residue 899 SER Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 949 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 300 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A1011 GLN B 112 GLN B 241 GLN ** B 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 HIS C 415 ASN C 598 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24697 Z= 0.226 Angle : 0.544 6.753 33522 Z= 0.288 Chirality : 0.040 0.154 3918 Planarity : 0.004 0.054 4275 Dihedral : 7.858 59.575 3608 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.55 % Allowed : 20.12 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.15), residues: 3136 helix: 1.88 (0.13), residues: 1667 sheet: 0.14 (0.24), residues: 436 loop : -0.57 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 864 HIS 0.004 0.000 HIS B 694 PHE 0.014 0.001 PHE A 459 TYR 0.019 0.001 TYR C 897 ARG 0.006 0.000 ARG C 535 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 607 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5971 (ttt) cc_final: 0.5634 (tpp) REVERT: A 34 GLN cc_start: 0.7236 (tt0) cc_final: 0.6912 (tt0) REVERT: A 95 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6355 (mt-10) REVERT: A 101 ASP cc_start: 0.7960 (m-30) cc_final: 0.7703 (m-30) REVERT: A 112 GLN cc_start: 0.7982 (tt0) cc_final: 0.7592 (mt0) REVERT: A 155 LYS cc_start: 0.8259 (mttt) cc_final: 0.7787 (mtmm) REVERT: A 193 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7854 (mt) REVERT: A 284 LYS cc_start: 0.7324 (mttt) cc_final: 0.6958 (mmmm) REVERT: A 312 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6198 (mm-30) REVERT: A 315 LYS cc_start: 0.7380 (mttt) cc_final: 0.7075 (mttp) REVERT: A 323 ASP cc_start: 0.7627 (t70) cc_final: 0.6852 (p0) REVERT: A 338 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6853 (mt-10) REVERT: A 342 HIS cc_start: 0.5764 (t70) cc_final: 0.5132 (m-70) REVERT: A 346 GLU cc_start: 0.6594 (mt-10) cc_final: 0.5969 (mt-10) REVERT: A 349 ILE cc_start: 0.6921 (mm) cc_final: 0.6322 (mt) REVERT: A 353 ILE cc_start: 0.6880 (mm) cc_final: 0.6597 (mt) REVERT: A 390 ILE cc_start: 0.7487 (mt) cc_final: 0.7247 (mm) REVERT: A 410 ILE cc_start: 0.6191 (mm) cc_final: 0.5918 (mt) REVERT: A 429 THR cc_start: 0.7660 (m) cc_final: 0.7277 (t) REVERT: A 435 MET cc_start: 0.7287 (tpp) cc_final: 0.7056 (tpp) REVERT: A 468 ARG cc_start: 0.6765 (mtm-85) cc_final: 0.6187 (ttm-80) REVERT: A 478 MET cc_start: 0.6086 (mmp) cc_final: 0.5700 (mpm) REVERT: A 605 ASP cc_start: 0.6896 (p0) cc_final: 0.6494 (m-30) REVERT: A 608 GLU cc_start: 0.6742 (tt0) cc_final: 0.6498 (tm-30) REVERT: A 647 SER cc_start: 0.7270 (t) cc_final: 0.6982 (p) REVERT: A 653 MET cc_start: 0.6282 (mtp) cc_final: 0.5944 (mmt) REVERT: A 666 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6496 (ttp) REVERT: A 683 ASN cc_start: 0.7811 (t0) cc_final: 0.7320 (t0) REVERT: A 707 LEU cc_start: 0.5987 (mt) cc_final: 0.5749 (mm) REVERT: A 736 GLN cc_start: 0.6549 (mt0) cc_final: 0.6303 (mt0) REVERT: A 829 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7060 (mm110) REVERT: A 892 CYS cc_start: 0.7093 (m) cc_final: 0.6639 (m) REVERT: A 898 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7117 (tp30) REVERT: A 940 GLN cc_start: 0.6890 (mt0) cc_final: 0.6515 (mt0) REVERT: A 949 LEU cc_start: 0.7638 (tp) cc_final: 0.7361 (tm) REVERT: A 952 LYS cc_start: 0.7049 (tttt) cc_final: 0.6560 (ttpp) REVERT: A 960 PHE cc_start: 0.6466 (t80) cc_final: 0.5768 (t80) REVERT: A 1022 VAL cc_start: 0.7402 (p) cc_final: 0.7049 (m) REVERT: B 1 MET cc_start: 0.4079 (ttm) cc_final: 0.3847 (ttt) REVERT: B 20 MET cc_start: 0.6145 (mtt) cc_final: 0.5768 (tpp) REVERT: B 55 GLU cc_start: 0.7501 (tt0) cc_final: 0.7213 (tt0) REVERT: B 229 VAL cc_start: 0.7987 (p) cc_final: 0.7747 (m) REVERT: B 237 GLN cc_start: 0.7243 (tp40) cc_final: 0.6900 (tm130) REVERT: B 304 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.6089 (mt-10) REVERT: B 359 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5669 (mt) REVERT: B 363 ARG cc_start: 0.7237 (mtp85) cc_final: 0.6860 (mtt-85) REVERT: B 366 ILE cc_start: 0.8243 (tt) cc_final: 0.7875 (tp) REVERT: B 421 SER cc_start: 0.7929 (t) cc_final: 0.7548 (m) REVERT: B 522 PHE cc_start: 0.7665 (t80) cc_final: 0.7421 (t80) REVERT: B 530 GLN cc_start: 0.6456 (mt0) cc_final: 0.5930 (mt0) REVERT: B 536 MET cc_start: 0.6302 (ttm) cc_final: 0.6041 (ttt) REVERT: B 575 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.5272 (mpp) REVERT: B 695 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6082 (mm-30) REVERT: B 718 ARG cc_start: 0.5998 (ptt90) cc_final: 0.5688 (pmm-80) REVERT: B 749 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.7218 (t0) REVERT: B 768 ARG cc_start: 0.6162 (mtp85) cc_final: 0.5820 (ttp80) REVERT: B 786 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: B 798 GLU cc_start: 0.6978 (mp0) cc_final: 0.6631 (mp0) REVERT: B 807 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7610 (t) REVERT: B 882 TYR cc_start: 0.7048 (m-80) cc_final: 0.6727 (m-80) REVERT: B 887 LEU cc_start: 0.8215 (tp) cc_final: 0.7751 (tm) REVERT: B 964 LEU cc_start: 0.8065 (mt) cc_final: 0.7807 (mp) REVERT: B 987 ILE cc_start: 0.8092 (mt) cc_final: 0.7860 (mm) REVERT: B 997 VAL cc_start: 0.8400 (p) cc_final: 0.8053 (m) REVERT: B 1045 LYS cc_start: 0.6818 (mmmt) cc_final: 0.6511 (mttm) REVERT: C 8 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7435 (mtp85) REVERT: C 11 PHE cc_start: 0.8517 (t80) cc_final: 0.8101 (t80) REVERT: C 20 MET cc_start: 0.8093 (mtp) cc_final: 0.7769 (mtp) REVERT: C 66 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6452 (mt-10) REVERT: C 124 ARG cc_start: 0.7290 (mtm-85) cc_final: 0.7044 (mtt-85) REVERT: C 188 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8332 (mt) REVERT: C 192 LYS cc_start: 0.7635 (mttt) cc_final: 0.6944 (mtpt) REVERT: C 197 GLN cc_start: 0.7660 (mp10) cc_final: 0.7111 (mp10) REVERT: C 242 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8478 (p) REVERT: C 261 ARG cc_start: 0.7705 (mtt-85) cc_final: 0.7102 (mmm160) REVERT: C 329 THR cc_start: 0.8308 (m) cc_final: 0.7896 (p) REVERT: C 346 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6693 (mt-10) REVERT: C 365 THR cc_start: 0.7659 (t) cc_final: 0.7226 (m) REVERT: C 370 LEU cc_start: 0.8514 (mt) cc_final: 0.8181 (mp) REVERT: C 398 MET cc_start: 0.8275 (tpp) cc_final: 0.8014 (tpp) REVERT: C 420 MET cc_start: 0.8249 (mtp) cc_final: 0.7862 (mtt) REVERT: C 445 ILE cc_start: 0.8161 (mt) cc_final: 0.7832 (mm) REVERT: C 478 MET cc_start: 0.8523 (mmm) cc_final: 0.8066 (mmp) REVERT: C 591 LYS cc_start: 0.7563 (mtpt) cc_final: 0.7138 (mttt) REVERT: C 601 MET cc_start: 0.8512 (mtm) cc_final: 0.7994 (mtp) REVERT: C 602 ASN cc_start: 0.7397 (t0) cc_final: 0.6973 (t0) REVERT: C 653 MET cc_start: 0.8408 (tpt) cc_final: 0.7988 (mmm) REVERT: C 657 MET cc_start: 0.6754 (mmm) cc_final: 0.6509 (tmm) REVERT: C 695 GLU cc_start: 0.6600 (tt0) cc_final: 0.6330 (pm20) REVERT: C 696 LYS cc_start: 0.8031 (mptp) cc_final: 0.7654 (mmtp) REVERT: C 731 ASN cc_start: 0.7539 (t0) cc_final: 0.7001 (m-40) REVERT: C 771 LYS cc_start: 0.8299 (mttp) cc_final: 0.7988 (mttm) REVERT: C 783 MET cc_start: 0.7310 (mmm) cc_final: 0.7039 (mmm) REVERT: C 880 PHE cc_start: 0.7433 (m-80) cc_final: 0.6606 (t80) REVERT: C 887 LEU cc_start: 0.7863 (tt) cc_final: 0.7604 (tp) REVERT: C 892 CYS cc_start: 0.7520 (m) cc_final: 0.7034 (m) REVERT: C 955 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7808 (tp) REVERT: C 963 GLU cc_start: 0.6951 (tt0) cc_final: 0.6610 (tt0) REVERT: C 977 HIS cc_start: 0.6968 (t-90) cc_final: 0.6541 (t-170) outliers start: 92 outliers final: 63 residues processed: 658 average time/residue: 2.1897 time to fit residues: 1760.6560 Evaluate side-chains 674 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 598 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 724 ASP Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 749 ASN Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 963 GLU Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 955 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 191 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A 953 ASN A1011 GLN B 112 GLN B 241 GLN ** B 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 HIS C 106 GLN C 415 ASN C 436 GLN C 598 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24697 Z= 0.326 Angle : 0.586 6.968 33522 Z= 0.312 Chirality : 0.042 0.169 3918 Planarity : 0.005 0.052 4275 Dihedral : 8.008 59.937 3608 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.13 % Allowed : 19.34 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 3136 helix: 1.75 (0.13), residues: 1663 sheet: 0.05 (0.23), residues: 450 loop : -0.68 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 362 HIS 0.005 0.001 HIS B 694 PHE 0.017 0.002 PHE A 459 TYR 0.017 0.002 TYR C 897 ARG 0.007 0.000 ARG C 535 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 595 time to evaluate : 3.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5916 (ttt) cc_final: 0.5597 (tpp) REVERT: A 34 GLN cc_start: 0.7145 (tt0) cc_final: 0.6797 (tt0) REVERT: A 95 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6434 (mt-10) REVERT: A 101 ASP cc_start: 0.8097 (m-30) cc_final: 0.7836 (m-30) REVERT: A 112 GLN cc_start: 0.8082 (tt0) cc_final: 0.7702 (mt0) REVERT: A 155 LYS cc_start: 0.8273 (mttt) cc_final: 0.7799 (mtmm) REVERT: A 193 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7858 (mt) REVERT: A 263 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7784 (ptpt) REVERT: A 284 LYS cc_start: 0.7367 (mttt) cc_final: 0.6943 (mmmm) REVERT: A 312 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6196 (mm-30) REVERT: A 315 LYS cc_start: 0.7370 (mttt) cc_final: 0.6998 (mttp) REVERT: A 323 ASP cc_start: 0.7723 (t70) cc_final: 0.6897 (p0) REVERT: A 338 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6880 (mt-10) REVERT: A 342 HIS cc_start: 0.5767 (t70) cc_final: 0.5174 (m-70) REVERT: A 346 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6014 (mt-10) REVERT: A 349 ILE cc_start: 0.6970 (mm) cc_final: 0.6362 (mt) REVERT: A 353 ILE cc_start: 0.6910 (mm) cc_final: 0.6626 (mt) REVERT: A 390 ILE cc_start: 0.7557 (mt) cc_final: 0.7324 (mm) REVERT: A 410 ILE cc_start: 0.6279 (mm) cc_final: 0.5997 (mt) REVERT: A 429 THR cc_start: 0.7678 (m) cc_final: 0.7298 (t) REVERT: A 435 MET cc_start: 0.7302 (tpp) cc_final: 0.7061 (tpp) REVERT: A 468 ARG cc_start: 0.6770 (mtm-85) cc_final: 0.6211 (ttm-80) REVERT: A 478 MET cc_start: 0.6071 (mmp) cc_final: 0.5724 (mpm) REVERT: A 608 GLU cc_start: 0.6710 (tt0) cc_final: 0.6495 (tm-30) REVERT: A 647 SER cc_start: 0.7341 (t) cc_final: 0.7098 (m) REVERT: A 653 MET cc_start: 0.6290 (mtp) cc_final: 0.5942 (mmt) REVERT: A 666 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6499 (ttp) REVERT: A 707 LEU cc_start: 0.5982 (mt) cc_final: 0.5740 (mm) REVERT: A 736 GLN cc_start: 0.6553 (mt0) cc_final: 0.6289 (mt0) REVERT: A 846 GLU cc_start: 0.6495 (mt-10) cc_final: 0.5976 (mm-30) REVERT: A 892 CYS cc_start: 0.7040 (m) cc_final: 0.6627 (m) REVERT: A 898 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7033 (tp30) REVERT: A 940 GLN cc_start: 0.6920 (mt0) cc_final: 0.6559 (mt0) REVERT: A 949 LEU cc_start: 0.7646 (tp) cc_final: 0.7340 (tm) REVERT: A 952 LYS cc_start: 0.7039 (tttt) cc_final: 0.6478 (ttpp) REVERT: A 960 PHE cc_start: 0.6449 (t80) cc_final: 0.5762 (t80) REVERT: A 1022 VAL cc_start: 0.7419 (p) cc_final: 0.7063 (m) REVERT: B 20 MET cc_start: 0.6153 (mtt) cc_final: 0.5785 (tpp) REVERT: B 55 GLU cc_start: 0.7516 (tt0) cc_final: 0.7228 (tt0) REVERT: B 87 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: B 229 VAL cc_start: 0.7992 (p) cc_final: 0.7756 (m) REVERT: B 237 GLN cc_start: 0.7237 (tp40) cc_final: 0.6914 (tm130) REVERT: B 304 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.6088 (mt-10) REVERT: B 335 LEU cc_start: 0.6709 (mt) cc_final: 0.6470 (mp) REVERT: B 359 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5804 (mt) REVERT: B 363 ARG cc_start: 0.7203 (mtp85) cc_final: 0.6853 (mtt-85) REVERT: B 366 ILE cc_start: 0.8248 (tt) cc_final: 0.7881 (tp) REVERT: B 420 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8148 (mtm) REVERT: B 421 SER cc_start: 0.7986 (OUTLIER) cc_final: 0.7603 (m) REVERT: B 522 PHE cc_start: 0.7664 (t80) cc_final: 0.7422 (t80) REVERT: B 530 GLN cc_start: 0.6440 (mt0) cc_final: 0.5906 (mt0) REVERT: B 536 MET cc_start: 0.6303 (ttm) cc_final: 0.6044 (ttt) REVERT: B 575 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.5290 (mpp) REVERT: B 695 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.6088 (mm-30) REVERT: B 718 ARG cc_start: 0.5994 (ptt90) cc_final: 0.5677 (pmm-80) REVERT: B 749 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7281 (t0) REVERT: B 751 MET cc_start: 0.8239 (ptt) cc_final: 0.7890 (ptt) REVERT: B 768 ARG cc_start: 0.6174 (mtp85) cc_final: 0.5830 (ttp80) REVERT: B 786 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: B 798 GLU cc_start: 0.6984 (mp0) cc_final: 0.6638 (mp0) REVERT: B 807 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7592 (t) REVERT: B 882 TYR cc_start: 0.7103 (m-80) cc_final: 0.6829 (m-80) REVERT: B 887 LEU cc_start: 0.8220 (tp) cc_final: 0.7745 (tm) REVERT: B 964 LEU cc_start: 0.8073 (mt) cc_final: 0.7804 (mp) REVERT: B 987 ILE cc_start: 0.8108 (mt) cc_final: 0.7896 (mm) REVERT: B 997 VAL cc_start: 0.8386 (p) cc_final: 0.8063 (m) REVERT: B 1045 LYS cc_start: 0.6822 (mmmt) cc_final: 0.6507 (mttm) REVERT: C 8 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7446 (mtp85) REVERT: C 11 PHE cc_start: 0.8547 (t80) cc_final: 0.8126 (t80) REVERT: C 20 MET cc_start: 0.8155 (mtp) cc_final: 0.7817 (mtp) REVERT: C 66 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6459 (mt-10) REVERT: C 124 ARG cc_start: 0.7232 (mtm-85) cc_final: 0.7026 (mtt-85) REVERT: C 188 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8335 (mt) REVERT: C 192 LYS cc_start: 0.7709 (mttt) cc_final: 0.7007 (mtpt) REVERT: C 197 GLN cc_start: 0.7611 (mp10) cc_final: 0.7108 (mp10) REVERT: C 242 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8452 (p) REVERT: C 261 ARG cc_start: 0.7710 (mtt-85) cc_final: 0.7033 (mmm160) REVERT: C 346 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6725 (mt-10) REVERT: C 365 THR cc_start: 0.7766 (t) cc_final: 0.7323 (m) REVERT: C 370 LEU cc_start: 0.8525 (mt) cc_final: 0.8165 (mm) REVERT: C 398 MET cc_start: 0.8261 (tpp) cc_final: 0.8032 (tpp) REVERT: C 414 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.6728 (tp30) REVERT: C 436 GLN cc_start: 0.6991 (tp40) cc_final: 0.6643 (tm130) REVERT: C 445 ILE cc_start: 0.8193 (mt) cc_final: 0.7866 (mm) REVERT: C 478 MET cc_start: 0.8537 (mmm) cc_final: 0.8101 (mmp) REVERT: C 591 LYS cc_start: 0.7596 (mtpt) cc_final: 0.7176 (mttt) REVERT: C 601 MET cc_start: 0.8516 (mtm) cc_final: 0.7994 (mtp) REVERT: C 602 ASN cc_start: 0.7425 (t0) cc_final: 0.7052 (t0) REVERT: C 603 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6316 (mm-30) REVERT: C 657 MET cc_start: 0.6772 (mmm) cc_final: 0.6508 (tmm) REVERT: C 695 GLU cc_start: 0.6616 (tt0) cc_final: 0.6331 (pm20) REVERT: C 696 LYS cc_start: 0.8035 (mptp) cc_final: 0.7659 (mmtp) REVERT: C 731 ASN cc_start: 0.7535 (t0) cc_final: 0.6997 (m-40) REVERT: C 771 LYS cc_start: 0.8314 (mttp) cc_final: 0.7989 (mttm) REVERT: C 783 MET cc_start: 0.7364 (mmm) cc_final: 0.7098 (mmm) REVERT: C 880 PHE cc_start: 0.7456 (m-80) cc_final: 0.6615 (t80) REVERT: C 887 LEU cc_start: 0.7894 (tt) cc_final: 0.7671 (tp) REVERT: C 949 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8163 (tp) REVERT: C 955 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7927 (tp) REVERT: C 963 GLU cc_start: 0.6955 (tt0) cc_final: 0.6585 (tt0) REVERT: C 977 HIS cc_start: 0.6975 (t-90) cc_final: 0.6516 (t-170) outliers start: 107 outliers final: 76 residues processed: 657 average time/residue: 2.2192 time to fit residues: 1783.9139 Evaluate side-chains 685 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 589 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 724 ASP Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 749 ASN Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 963 GLU Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain C residue 899 SER Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 949 LEU Chi-restraints excluded: chain C residue 955 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 280 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 220 optimal weight: 0.0170 chunk 85 optimal weight: 8.9990 chunk 253 optimal weight: 6.9990 chunk 265 optimal weight: 9.9990 chunk 279 optimal weight: 1.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A 953 ASN A1011 GLN B 104 GLN B 112 GLN B 241 GLN ** B 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 HIS C 415 ASN C 598 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24697 Z= 0.247 Angle : 0.549 6.430 33522 Z= 0.290 Chirality : 0.041 0.236 3918 Planarity : 0.004 0.056 4275 Dihedral : 7.688 59.884 3608 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.63 % Allowed : 20.27 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.28 (0.15), residues: 3136 helix: 1.93 (0.13), residues: 1665 sheet: 0.08 (0.23), residues: 446 loop : -0.56 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 362 HIS 0.004 0.001 HIS B 694 PHE 0.014 0.001 PHE A 459 TYR 0.015 0.002 TYR C 897 ARG 0.008 0.000 ARG C 535 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 589 time to evaluate : 3.819 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: A 1 MET cc_start: 0.5908 (ttt) cc_final: 0.5587 (tpp) REVERT: A 34 GLN cc_start: 0.7183 (tt0) cc_final: 0.6825 (tt0) REVERT: A 95 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6368 (mt-10) REVERT: A 101 ASP cc_start: 0.7951 (m-30) cc_final: 0.7720 (m-30) REVERT: A 112 GLN cc_start: 0.7982 (tt0) cc_final: 0.7584 (mt0) REVERT: A 155 LYS cc_start: 0.8257 (mttt) cc_final: 0.7780 (mtmm) REVERT: A 193 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7853 (mt) REVERT: A 263 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7664 (ptpt) REVERT: A 284 LYS cc_start: 0.7316 (mttt) cc_final: 0.6947 (mmmm) REVERT: A 312 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6172 (mm-30) REVERT: A 315 LYS cc_start: 0.7370 (mttt) cc_final: 0.7021 (mttp) REVERT: A 323 ASP cc_start: 0.7564 (t70) cc_final: 0.6949 (p0) REVERT: A 342 HIS cc_start: 0.5762 (t70) cc_final: 0.5133 (m-70) REVERT: A 346 GLU cc_start: 0.6593 (mt-10) cc_final: 0.5970 (mt-10) REVERT: A 349 ILE cc_start: 0.6952 (mm) cc_final: 0.6336 (mt) REVERT: A 353 ILE cc_start: 0.6898 (mm) cc_final: 0.6613 (mt) REVERT: A 390 ILE cc_start: 0.7531 (mt) cc_final: 0.7304 (mm) REVERT: A 410 ILE cc_start: 0.6268 (mm) cc_final: 0.5990 (mt) REVERT: A 429 THR cc_start: 0.7665 (m) cc_final: 0.7273 (t) REVERT: A 435 MET cc_start: 0.7249 (tpp) cc_final: 0.7022 (tpp) REVERT: A 468 ARG cc_start: 0.6787 (mtm-85) cc_final: 0.6282 (ttm-80) REVERT: A 478 MET cc_start: 0.6067 (mmp) cc_final: 0.5728 (mpm) REVERT: A 605 ASP cc_start: 0.6904 (p0) cc_final: 0.6527 (m-30) REVERT: A 608 GLU cc_start: 0.6721 (tt0) cc_final: 0.6493 (tm-30) REVERT: A 642 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6273 (mp0) REVERT: A 653 MET cc_start: 0.6282 (mtp) cc_final: 0.5935 (mmt) REVERT: A 666 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6465 (ttp) REVERT: A 683 ASN cc_start: 0.7775 (t0) cc_final: 0.7364 (t0) REVERT: A 707 LEU cc_start: 0.5972 (mt) cc_final: 0.5731 (mm) REVERT: A 736 GLN cc_start: 0.6571 (mt0) cc_final: 0.6275 (mt0) REVERT: A 829 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7098 (mm-40) REVERT: A 846 GLU cc_start: 0.6237 (mt-10) cc_final: 0.5796 (mm-30) REVERT: A 862 TYR cc_start: 0.7071 (p90) cc_final: 0.6773 (p90) REVERT: A 892 CYS cc_start: 0.7105 (m) cc_final: 0.6649 (m) REVERT: A 898 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7066 (tp30) REVERT: A 940 GLN cc_start: 0.6888 (mt0) cc_final: 0.6524 (mt0) REVERT: A 949 LEU cc_start: 0.7619 (tp) cc_final: 0.7357 (tm) REVERT: A 952 LYS cc_start: 0.7025 (tttt) cc_final: 0.6567 (ttpp) REVERT: A 960 PHE cc_start: 0.6450 (t80) cc_final: 0.5800 (t80) REVERT: A 1022 VAL cc_start: 0.7419 (p) cc_final: 0.7065 (m) REVERT: B 1 MET cc_start: 0.4067 (ttm) cc_final: 0.3838 (ttt) REVERT: B 8 ARG cc_start: 0.7604 (mtt90) cc_final: 0.7326 (mtt90) REVERT: B 20 MET cc_start: 0.6145 (mtt) cc_final: 0.5780 (tpp) REVERT: B 55 GLU cc_start: 0.7510 (tt0) cc_final: 0.7219 (tt0) REVERT: B 87 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8192 (mt0) REVERT: B 229 VAL cc_start: 0.7968 (p) cc_final: 0.7736 (m) REVERT: B 237 GLN cc_start: 0.7266 (tp40) cc_final: 0.6931 (tm130) REVERT: B 304 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.6078 (mt-10) REVERT: B 359 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5634 (mt) REVERT: B 363 ARG cc_start: 0.7461 (mtp85) cc_final: 0.7094 (mtt-85) REVERT: B 366 ILE cc_start: 0.8244 (tt) cc_final: 0.7868 (tp) REVERT: B 420 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8085 (mtm) REVERT: B 421 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7563 (m) REVERT: B 433 ARG cc_start: 0.6721 (ttt-90) cc_final: 0.6397 (ttt-90) REVERT: B 522 PHE cc_start: 0.7654 (t80) cc_final: 0.7404 (t80) REVERT: B 530 GLN cc_start: 0.6412 (mt0) cc_final: 0.5899 (mt0) REVERT: B 536 MET cc_start: 0.6297 (ttm) cc_final: 0.6038 (ttt) REVERT: B 575 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.5277 (mpp) REVERT: B 695 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.6085 (mm-30) REVERT: B 718 ARG cc_start: 0.6012 (ptt90) cc_final: 0.5681 (pmm-80) REVERT: B 749 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7238 (t0) REVERT: B 751 MET cc_start: 0.8233 (ptt) cc_final: 0.7900 (ptt) REVERT: B 768 ARG cc_start: 0.6174 (mtp85) cc_final: 0.5861 (ttp80) REVERT: B 786 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: B 798 GLU cc_start: 0.6972 (mp0) cc_final: 0.6625 (mp0) REVERT: B 807 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7606 (t) REVERT: B 882 TYR cc_start: 0.7071 (m-80) cc_final: 0.6811 (m-80) REVERT: B 887 LEU cc_start: 0.8202 (tp) cc_final: 0.7721 (tm) REVERT: B 964 LEU cc_start: 0.8063 (mt) cc_final: 0.7806 (mp) REVERT: B 997 VAL cc_start: 0.8429 (p) cc_final: 0.8094 (m) REVERT: B 1045 LYS cc_start: 0.6841 (mmmt) cc_final: 0.6517 (mttm) REVERT: C 8 ARG cc_start: 0.7653 (mtp85) cc_final: 0.7430 (mtt-85) REVERT: C 11 PHE cc_start: 0.8518 (t80) cc_final: 0.8121 (t80) REVERT: C 20 MET cc_start: 0.8086 (mtp) cc_final: 0.7751 (mtp) REVERT: C 66 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6425 (mt-10) REVERT: C 124 ARG cc_start: 0.7223 (mtm-85) cc_final: 0.7020 (mtt-85) REVERT: C 188 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8340 (mt) REVERT: C 192 LYS cc_start: 0.7693 (mttt) cc_final: 0.6993 (mtpt) REVERT: C 197 GLN cc_start: 0.7640 (mp10) cc_final: 0.7002 (mp-120) REVERT: C 242 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8477 (p) REVERT: C 261 ARG cc_start: 0.7762 (mtt-85) cc_final: 0.7148 (mmm160) REVERT: C 346 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6683 (mt-10) REVERT: C 365 THR cc_start: 0.7678 (t) cc_final: 0.7248 (m) REVERT: C 370 LEU cc_start: 0.8528 (mt) cc_final: 0.8174 (mm) REVERT: C 398 MET cc_start: 0.8265 (tpp) cc_final: 0.8012 (tpp) REVERT: C 420 MET cc_start: 0.8260 (mtp) cc_final: 0.7955 (mtt) REVERT: C 445 ILE cc_start: 0.8144 (mt) cc_final: 0.7857 (mm) REVERT: C 478 MET cc_start: 0.8531 (mmm) cc_final: 0.8083 (mmp) REVERT: C 591 LYS cc_start: 0.7566 (mtpt) cc_final: 0.7146 (mttt) REVERT: C 601 MET cc_start: 0.8488 (mtm) cc_final: 0.7966 (mtp) REVERT: C 602 ASN cc_start: 0.7415 (t0) cc_final: 0.7031 (t0) REVERT: C 653 MET cc_start: 0.8417 (tpt) cc_final: 0.8012 (mmm) REVERT: C 657 MET cc_start: 0.6771 (mmm) cc_final: 0.6496 (tmm) REVERT: C 695 GLU cc_start: 0.6607 (tt0) cc_final: 0.6298 (pm20) REVERT: C 696 LYS cc_start: 0.8056 (mptp) cc_final: 0.7619 (mmtp) REVERT: C 731 ASN cc_start: 0.7542 (t0) cc_final: 0.6994 (m-40) REVERT: C 771 LYS cc_start: 0.8298 (mttp) cc_final: 0.7975 (mttm) REVERT: C 783 MET cc_start: 0.7369 (mmm) cc_final: 0.7108 (mmm) REVERT: C 880 PHE cc_start: 0.7445 (m-80) cc_final: 0.6613 (t80) REVERT: C 887 LEU cc_start: 0.7877 (tt) cc_final: 0.7648 (tp) REVERT: C 949 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8123 (tp) REVERT: C 955 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7874 (tp) REVERT: C 963 GLU cc_start: 0.6926 (tt0) cc_final: 0.6579 (tt0) REVERT: C 977 HIS cc_start: 0.6973 (t-90) cc_final: 0.6536 (t-170) outliers start: 94 outliers final: 67 residues processed: 642 average time/residue: 2.2140 time to fit residues: 1736.7860 Evaluate side-chains 672 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 586 time to evaluate : 3.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 724 ASP Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 749 ASN Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 963 GLU Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain C residue 899 SER Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 949 LEU Chi-restraints excluded: chain C residue 955 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A1011 GLN B 176 GLN B 241 GLN ** B 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 HIS C 415 ASN C 436 GLN C 598 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24697 Z= 0.283 Angle : 0.567 6.310 33522 Z= 0.300 Chirality : 0.041 0.155 3918 Planarity : 0.005 0.057 4275 Dihedral : 7.730 59.744 3608 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.59 % Allowed : 20.69 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3136 helix: 1.85 (0.13), residues: 1668 sheet: -0.02 (0.23), residues: 455 loop : -0.64 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 362 HIS 0.004 0.001 HIS B 694 PHE 0.016 0.002 PHE B 332 TYR 0.015 0.002 TYR C 820 ARG 0.008 0.000 ARG C 535 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 590 time to evaluate : 3.765 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: A 1 MET cc_start: 0.5880 (ttt) cc_final: 0.5581 (tpp) REVERT: A 34 GLN cc_start: 0.7132 (tt0) cc_final: 0.6771 (tt0) REVERT: A 95 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6442 (mt-10) REVERT: A 101 ASP cc_start: 0.7962 (m-30) cc_final: 0.7732 (m-30) REVERT: A 112 GLN cc_start: 0.8064 (tt0) cc_final: 0.7698 (mt0) REVERT: A 155 LYS cc_start: 0.8261 (mttt) cc_final: 0.7783 (mtmm) REVERT: A 193 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7847 (mt) REVERT: A 284 LYS cc_start: 0.7345 (mttt) cc_final: 0.6977 (mmmm) REVERT: A 312 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6190 (mm-30) REVERT: A 315 LYS cc_start: 0.7356 (mttt) cc_final: 0.6996 (mttp) REVERT: A 323 ASP cc_start: 0.7575 (t70) cc_final: 0.6974 (p0) REVERT: A 338 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6713 (mt-10) REVERT: A 342 HIS cc_start: 0.5771 (t70) cc_final: 0.5160 (m-70) REVERT: A 346 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6002 (mt-10) REVERT: A 349 ILE cc_start: 0.6933 (mm) cc_final: 0.6332 (mt) REVERT: A 353 ILE cc_start: 0.6860 (mm) cc_final: 0.6576 (mt) REVERT: A 390 ILE cc_start: 0.7486 (mt) cc_final: 0.7246 (mm) REVERT: A 429 THR cc_start: 0.7632 (m) cc_final: 0.7238 (t) REVERT: A 435 MET cc_start: 0.7279 (tpp) cc_final: 0.7036 (tpp) REVERT: A 468 ARG cc_start: 0.6795 (mtm-85) cc_final: 0.6290 (ttm-80) REVERT: A 478 MET cc_start: 0.6091 (mmp) cc_final: 0.5763 (mpm) REVERT: A 605 ASP cc_start: 0.6943 (p0) cc_final: 0.6548 (m-30) REVERT: A 608 GLU cc_start: 0.6730 (tt0) cc_final: 0.6496 (tm-30) REVERT: A 653 MET cc_start: 0.6287 (mtp) cc_final: 0.5929 (mmt) REVERT: A 666 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6433 (ttp) REVERT: A 683 ASN cc_start: 0.7772 (t0) cc_final: 0.7557 (t0) REVERT: A 707 LEU cc_start: 0.5967 (mt) cc_final: 0.5728 (mm) REVERT: A 736 GLN cc_start: 0.6574 (mt0) cc_final: 0.6257 (mt0) REVERT: A 846 GLU cc_start: 0.6274 (mt-10) cc_final: 0.5839 (mm-30) REVERT: A 862 TYR cc_start: 0.7119 (p90) cc_final: 0.6851 (p90) REVERT: A 892 CYS cc_start: 0.7043 (m) cc_final: 0.6606 (m) REVERT: A 898 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7015 (tp30) REVERT: A 940 GLN cc_start: 0.6908 (mt0) cc_final: 0.6586 (mt0) REVERT: A 949 LEU cc_start: 0.7642 (tp) cc_final: 0.7369 (tm) REVERT: A 952 LYS cc_start: 0.7046 (tttt) cc_final: 0.6490 (ttpp) REVERT: A 960 PHE cc_start: 0.6437 (t80) cc_final: 0.5795 (t80) REVERT: A 1022 VAL cc_start: 0.7420 (p) cc_final: 0.7065 (m) REVERT: B 8 ARG cc_start: 0.7543 (mtt90) cc_final: 0.7256 (mtt90) REVERT: B 20 MET cc_start: 0.6136 (mtt) cc_final: 0.5782 (tpp) REVERT: B 55 GLU cc_start: 0.7512 (tt0) cc_final: 0.7209 (tt0) REVERT: B 87 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: B 229 VAL cc_start: 0.7966 (p) cc_final: 0.7735 (m) REVERT: B 237 GLN cc_start: 0.7235 (tp40) cc_final: 0.6916 (tm130) REVERT: B 304 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6077 (mt-10) REVERT: B 359 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5694 (mt) REVERT: B 363 ARG cc_start: 0.7456 (mtp85) cc_final: 0.7100 (mtt-85) REVERT: B 366 ILE cc_start: 0.8241 (tt) cc_final: 0.7868 (tp) REVERT: B 395 MET cc_start: 0.7814 (mmt) cc_final: 0.7604 (mmt) REVERT: B 420 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8106 (mtm) REVERT: B 421 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7565 (m) REVERT: B 433 ARG cc_start: 0.6723 (ttt-90) cc_final: 0.6399 (ttt-90) REVERT: B 530 GLN cc_start: 0.6429 (mt0) cc_final: 0.5807 (mt0) REVERT: B 536 MET cc_start: 0.6299 (ttm) cc_final: 0.6044 (ttt) REVERT: B 575 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.5227 (mpp) REVERT: B 695 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6085 (mm-30) REVERT: B 718 ARG cc_start: 0.6002 (ptt90) cc_final: 0.5678 (pmm-80) REVERT: B 749 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7268 (t0) REVERT: B 751 MET cc_start: 0.8207 (ptt) cc_final: 0.7869 (ptt) REVERT: B 768 ARG cc_start: 0.6184 (mtp85) cc_final: 0.5867 (ttp80) REVERT: B 786 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: B 798 GLU cc_start: 0.6960 (mp0) cc_final: 0.6607 (mp0) REVERT: B 807 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7599 (t) REVERT: B 882 TYR cc_start: 0.7053 (m-80) cc_final: 0.6826 (m-80) REVERT: B 887 LEU cc_start: 0.8201 (tp) cc_final: 0.7719 (tm) REVERT: B 964 LEU cc_start: 0.8066 (mt) cc_final: 0.7810 (mp) REVERT: B 997 VAL cc_start: 0.8433 (p) cc_final: 0.8125 (m) REVERT: B 1045 LYS cc_start: 0.6819 (mmmt) cc_final: 0.6509 (mttm) REVERT: C 8 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7449 (mtt-85) REVERT: C 11 PHE cc_start: 0.8532 (t80) cc_final: 0.8144 (t80) REVERT: C 20 MET cc_start: 0.8095 (mtp) cc_final: 0.7754 (mtp) REVERT: C 66 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6390 (mt-10) REVERT: C 124 ARG cc_start: 0.7306 (mtm-85) cc_final: 0.7059 (mtt-85) REVERT: C 188 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8325 (mt) REVERT: C 192 LYS cc_start: 0.7696 (mttt) cc_final: 0.6993 (mtpt) REVERT: C 197 GLN cc_start: 0.7639 (mp10) cc_final: 0.7113 (mp10) REVERT: C 242 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8461 (p) REVERT: C 261 ARG cc_start: 0.7764 (mtt-85) cc_final: 0.7077 (mmm160) REVERT: C 346 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6701 (mt-10) REVERT: C 365 THR cc_start: 0.7715 (t) cc_final: 0.7287 (m) REVERT: C 370 LEU cc_start: 0.8526 (mt) cc_final: 0.8166 (mm) REVERT: C 398 MET cc_start: 0.8268 (tpp) cc_final: 0.8028 (tpp) REVERT: C 420 MET cc_start: 0.8248 (mtp) cc_final: 0.7844 (mtt) REVERT: C 436 GLN cc_start: 0.6986 (tp40) cc_final: 0.6629 (tm130) REVERT: C 445 ILE cc_start: 0.8196 (mt) cc_final: 0.7904 (mm) REVERT: C 478 MET cc_start: 0.8543 (mmm) cc_final: 0.8097 (mmp) REVERT: C 591 LYS cc_start: 0.7605 (mtpt) cc_final: 0.7175 (mttt) REVERT: C 601 MET cc_start: 0.8492 (mtm) cc_final: 0.7890 (mtp) REVERT: C 602 ASN cc_start: 0.7427 (t0) cc_final: 0.7067 (t0) REVERT: C 657 MET cc_start: 0.6794 (mmm) cc_final: 0.6500 (tmm) REVERT: C 695 GLU cc_start: 0.6613 (tt0) cc_final: 0.6300 (pm20) REVERT: C 696 LYS cc_start: 0.8102 (mptp) cc_final: 0.7668 (mmtp) REVERT: C 731 ASN cc_start: 0.7512 (t0) cc_final: 0.7005 (m-40) REVERT: C 771 LYS cc_start: 0.8301 (mttp) cc_final: 0.7978 (mttm) REVERT: C 783 MET cc_start: 0.7383 (mmm) cc_final: 0.7127 (mmm) REVERT: C 880 PHE cc_start: 0.7427 (m-80) cc_final: 0.6639 (t80) REVERT: C 887 LEU cc_start: 0.7894 (tt) cc_final: 0.7665 (tp) REVERT: C 949 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8167 (tp) REVERT: C 955 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7878 (tp) REVERT: C 963 GLU cc_start: 0.6941 (tt0) cc_final: 0.6607 (tt0) REVERT: C 977 HIS cc_start: 0.6977 (t-90) cc_final: 0.6536 (t-170) outliers start: 93 outliers final: 70 residues processed: 644 average time/residue: 2.1999 time to fit residues: 1727.2202 Evaluate side-chains 675 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 587 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 724 ASP Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 749 ASN Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 963 GLU Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain C residue 899 SER Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 949 LEU Chi-restraints excluded: chain C residue 955 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 254 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 112 GLN B 176 GLN B 241 GLN ** B 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 HIS C 415 ASN C 598 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.148120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.124580 restraints weight = 72243.119| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 0.97 r_work: 0.3075 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24697 Z= 0.244 Angle : 0.546 6.065 33522 Z= 0.288 Chirality : 0.041 0.170 3918 Planarity : 0.004 0.058 4275 Dihedral : 7.558 59.956 3608 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.40 % Allowed : 20.89 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.15), residues: 3136 helix: 1.97 (0.13), residues: 1665 sheet: 0.05 (0.23), residues: 450 loop : -0.57 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 362 HIS 0.004 0.001 HIS B 694 PHE 0.017 0.001 PHE B 332 TYR 0.014 0.002 TYR C 897 ARG 0.008 0.000 ARG C 535 =============================================================================== Job complete usr+sys time: 22967.38 seconds wall clock time: 399 minutes 44.72 seconds (23984.72 seconds total)