Starting phenix.real_space_refine on Sun Feb 25 04:48:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4p_23663/02_2024/7m4p_23663_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4p_23663/02_2024/7m4p_23663.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4p_23663/02_2024/7m4p_23663_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4p_23663/02_2024/7m4p_23663_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4p_23663/02_2024/7m4p_23663_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4p_23663/02_2024/7m4p_23663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4p_23663/02_2024/7m4p_23663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4p_23663/02_2024/7m4p_23663_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4p_23663/02_2024/7m4p_23663_trim_updated.pdb" } resolution = 2.86 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= 0.202 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 S 102 5.16 5 C 15649 2.51 5 N 3982 2.21 5 O 4531 1.98 5 F 1 1.80 5 H 24343 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 ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 524": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 871": "OE1" <-> "OE2" Residue "A GLU 959": "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 ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 513": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 959": "OE1" <-> "OE2" Residue "B GLU 966": "OE1" <-> "OE2" Residue "B ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1041": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 524": "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 603": "OE1" <-> "OE2" Residue "C GLU 642": "OE1" <-> "OE2" 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 GLU 959": "OE1" <-> "OE2" Residue "C GLU 963": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 48616 Number of models: 1 Model: "" Number of chains: 6 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: 16091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 16091 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: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'3PE': 4, 'YQM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 62 Chain: "C" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 47 Time building chain proxies: 19.95, per 1000 atoms: 0.41 Number of scatterers: 48616 At special positions: 0 Unit cell: (126.36, 126.36, 157.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 102 16.00 P 8 15.00 F 1 9.00 O 4531 8.00 N 3982 7.00 C 15649 6.00 H 24343 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: 39.79 Conformation dependent library (CDL) restraints added in 5.3 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: 109 helices and 28 sheets defined 54.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.907A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 62 through 68 removed outlier: 4.261A pdb=" N GLN A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 removed outlier: 4.592A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A 117 " --> pdb=" O SER A 113 " (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 168 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 248 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: 4.311A pdb=" N LYS A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 4.947A 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: 4.730A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 458 removed outlier: 6.148A pdb=" N GLY A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 4.339A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 496 removed outlier: 4.347A 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: 3.792A pdb=" N PHE A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.752A pdb=" N GLN A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) 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: 4.062A pdb=" N ALA A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASN A 656 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET A 657 " --> pdb=" O MET A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.584A pdb=" N GLN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 744 through 755 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 786 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 851 Processing helix chain 'A' and resid 867 through 897 removed outlier: 4.263A pdb=" N ARG A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 874 " --> pdb=" O GLU A 870 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA A 878 " --> pdb=" O SER A 874 " (cutoff:3.500A) Proline residue: A 879 - end of helix removed outlier: 3.915A pdb=" N TYR A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 883 " --> pdb=" O PRO A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 928 removed outlier: 4.248A pdb=" N LEU A 908 " --> pdb=" O SER A 905 " (cutoff:3.500A) Proline residue: A 911 - end of helix removed outlier: 4.120A pdb=" N ILE A 915 " --> pdb=" O LEU A 912 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A 928 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 967 removed outlier: 3.874A pdb=" N LYS A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 1002 removed outlier: 4.981A 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 removed outlier: 3.671A pdb=" N LEU A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1043 removed outlier: 3.719A pdb=" N ILE A1030 " --> pdb=" O THR A1026 " (cutoff:3.500A) removed outlier: 4.387A 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 removed outlier: 3.580A pdb=" N ILE B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.881A pdb=" N THR B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 68 removed outlier: 4.112A pdb=" N GLN B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 117 removed outlier: 4.309A pdb=" N SER B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 167 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 314 removed outlier: 3.630A pdb=" N GLU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 358 Processing helix chain 'B' and resid 364 through 385 Proline residue: B 368 - end of helix removed outlier: 4.281A pdb=" N VAL B 372 " --> pdb=" O THR B 369 " (cutoff:3.500A) Proline residue: B 373 - end of helix removed outlier: 3.504A pdb=" N ILE B 383 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN B 384 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 423 removed outlier: 4.088A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 458 removed outlier: 5.452A pdb=" N GLY B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 4.285A pdb=" N PHE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 496 removed outlier: 3.803A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 4.735A 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 511 through 537 removed outlier: 3.736A pdb=" N GLY B 521 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 530 " --> pdb=" O HIS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' 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 Processing helix chain 'B' and resid 694 through 710 removed outlier: 3.518A pdb=" N GLN B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 744 through 756 Processing helix chain 'B' and resid 778 through 780 No H-bonds generated for 'chain 'B' and resid 778 through 780' 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 866 through 874 removed outlier: 3.768A pdb=" N GLU B 870 " --> pdb=" O GLY B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 897 Processing helix chain 'B' and resid 902 through 927 removed outlier: 3.684A pdb=" N LEU B 908 " --> pdb=" O SER B 905 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 910 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Proline residue: B 911 - end of helix removed outlier: 3.960A pdb=" N ILE B 915 " --> pdb=" O LEU B 912 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY B 916 " --> pdb=" O GLY B 913 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE B 927 " --> pdb=" O GLY B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 966 Processing helix chain 'B' and resid 971 through 1001 removed outlier: 4.773A 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: 3.532A pdb=" N GLY B1017 " --> pdb=" O SER B1013 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE B1031 " --> pdb=" O PHE B1027 " (cutoff:3.500A) Proline residue: B1034 - end of helix removed outlier: 3.595A pdb=" N ILE B1043 " --> pdb=" O TRP B1039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.992A pdb=" N HIS C 7 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 28 removed outlier: 3.643A pdb=" N THR C 28 " --> pdb=" O ILE C 24 " (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 116 removed outlier: 4.202A pdb=" N SER C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 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 248 Processing helix chain 'C' and resid 299 through 316 removed outlier: 4.391A pdb=" N LYS C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) removed outlier: 5.109A 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: 3.897A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.604A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix removed outlier: 3.557A pdb=" N PHE C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 405 removed outlier: 4.339A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.280A 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: 5.963A pdb=" N GLY C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) removed outlier: 5.505A 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 495 removed outlier: 3.778A pdb=" N GLN C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.415A 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 602 removed outlier: 3.624A pdb=" N PHE C 600 " --> pdb=" O MET C 596 " (cutoff:3.500A) 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: 3.840A pdb=" N ALA C 654 " --> pdb=" O GLN C 650 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN C 656 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N MET C 657 " --> pdb=" O MET C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 708 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 855 removed outlier: 4.039A pdb=" N LEU C 852 " --> pdb=" O ILE C 848 " (cutoff:3.500A) Proline residue: C 853 - end of helix Processing helix chain 'C' and resid 867 through 897 removed outlier: 3.705A pdb=" N GLN C 877 " --> pdb=" O GLU C 873 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA C 878 " --> pdb=" O SER C 874 " (cutoff:3.500A) Proline residue: C 879 - end of helix Processing helix chain 'C' and resid 901 through 928 removed outlier: 3.942A pdb=" N VAL C 909 " --> pdb=" O SER C 905 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 910 " --> pdb=" O VAL C 906 " (cutoff:3.500A) Proline residue: C 911 - end of helix removed outlier: 4.284A pdb=" N GLY C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 917 " --> pdb=" O GLY C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 968 removed outlier: 3.988A pdb=" N PHE C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 1001 removed outlier: 4.896A pdb=" N ARG C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) Proline residue: C 985 - end of helix Proline residue: C 999 - end of helix 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: 3.812A pdb=" N GLN A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.616A 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 324 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: 6.521A pdb=" N LYS A 631 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE A 610 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 629 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR A 612 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 627 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER A 614 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 7.001A 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 829 removed outlier: 3.654A pdb=" N LEU A 684 " --> pdb=" O ILE A 828 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 725 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: 6.585A 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: 3.905A pdb=" N GLN B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 322 through 328 removed outlier: 6.434A pdb=" N VAL B 139 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.619A 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 217 through 219 removed outlier: 3.956A pdb=" N GLY B 217 " --> pdb=" O VAL B 234 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 279 through 281 removed outlier: 6.587A pdb=" N LYS B 631 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 610 " --> pdb=" O PHE B 629 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE B 629 " --> pdb=" O ILE B 610 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 612 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 627 " --> pdb=" O THR B 612 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 825 through 830 Processing sheet with id= P, first strand: chain 'B' and resid 725 through 732 Processing sheet with id= Q, first strand: chain 'B' and resid 762 through 765 Processing sheet with id= R, first strand: chain 'B' and resid 791 through 793 Processing sheet with id= S, first strand: chain 'B' and resid 250 through 253 removed outlier: 7.046A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.600A pdb=" N GLN C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR C 77 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 322 through 328 removed outlier: 6.489A pdb=" N VAL C 139 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 266 through 272 Processing sheet with id= W, first strand: chain 'C' and resid 278 through 281 removed outlier: 6.857A pdb=" N LYS C 631 " --> pdb=" O GLU C 608 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 610 " --> pdb=" O PHE C 629 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE C 629 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR C 612 " --> pdb=" O ILE C 627 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 627 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N SER C 614 " --> pdb=" O ALA C 625 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA C 625 " --> pdb=" O SER C 614 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 825 through 830 removed outlier: 3.599A pdb=" N GLY C 830 " --> pdb=" O PHE C 682 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 724 through 729 Processing sheet with id= Z, first strand: chain 'C' and resid 762 through 765 Processing sheet with id= AA, first strand: chain 'C' and resid 791 through 793 Processing sheet with id= AB, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.772A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) 1377 hydrogen bonds defined for protein. 3840 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: 22.45 Time building geometry restraints manager: 41.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 24337 1.00 - 1.20: 224 1.20 - 1.41: 9585 1.41 - 1.61: 14728 1.61 - 1.81: 213 Bond restraints: 49087 Sorted by residual: bond pdb=" C14 YQM B1105 " pdb=" C15 YQM B1105 " ideal model delta sigma weight residual 1.035 1.546 -0.511 2.00e-02 2.50e+03 6.52e+02 bond pdb=" C08 YQM B1105 " pdb=" C09 YQM B1105 " ideal model delta sigma weight residual 1.951 1.561 0.390 2.00e-02 2.50e+03 3.81e+02 bond pdb=" C15 YQM B1105 " pdb=" C16 YQM B1105 " ideal model delta sigma weight residual 1.771 1.402 0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C07 YQM B1105 " pdb=" C16 YQM B1105 " ideal model delta sigma weight residual 1.184 1.505 -0.321 2.00e-02 2.50e+03 2.57e+02 bond pdb=" C06 YQM B1105 " pdb=" C07 YQM B1105 " ideal model delta sigma weight residual 1.876 1.569 0.307 2.00e-02 2.50e+03 2.35e+02 ... (remaining 49082 not shown) Histogram of bond angle deviations from ideal: 79.26 - 90.30: 7 90.30 - 101.34: 75 101.34 - 112.38: 57632 112.38 - 123.42: 27209 123.42 - 134.46: 3856 Bond angle restraints: 88779 Sorted by residual: angle pdb=" C ALA C 287 " pdb=" N GLY C 288 " pdb=" CA GLY C 288 " ideal model delta sigma weight residual 121.65 131.19 -9.54 6.80e-01 2.16e+00 1.97e+02 angle pdb=" CG LEU A 881 " pdb=" CD2 LEU A 881 " pdb="HD21 LEU A 881 " ideal model delta sigma weight residual 109.00 79.26 29.74 3.00e+00 1.11e-01 9.82e+01 angle pdb="HD21 LEU A 881 " pdb=" CD2 LEU A 881 " pdb="HD22 LEU A 881 " ideal model delta sigma weight residual 110.00 80.87 29.13 3.00e+00 1.11e-01 9.43e+01 angle pdb="HD22 LEU A 881 " pdb=" CD2 LEU A 881 " pdb="HD23 LEU A 881 " ideal model delta sigma weight residual 110.00 81.16 28.84 3.00e+00 1.11e-01 9.24e+01 angle pdb=" CG LEU A 881 " pdb=" CD2 LEU A 881 " pdb="HD23 LEU A 881 " ideal model delta sigma weight residual 109.00 80.18 28.82 3.00e+00 1.11e-01 9.23e+01 ... (remaining 88774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 21377 22.71 - 45.42: 1355 45.42 - 68.13: 484 68.13 - 90.84: 33 90.84 - 113.56: 1 Dihedral angle restraints: 23250 sinusoidal: 12831 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 -153.57 -26.43 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" N GLU B 675 " pdb=" C GLU B 675 " pdb=" CA GLU B 675 " pdb=" CB GLU B 675 " ideal model delta harmonic sigma weight residual 122.80 135.13 -12.33 0 2.50e+00 1.60e-01 2.43e+01 dihedral pdb=" C VAL B 454 " pdb=" N VAL B 454 " pdb=" CA VAL B 454 " pdb=" CB VAL B 454 " ideal model delta harmonic sigma weight residual -122.00 -133.53 11.53 0 2.50e+00 1.60e-01 2.13e+01 ... (remaining 23247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.292: 3902 0.292 - 0.585: 19 0.585 - 0.877: 0 0.877 - 1.169: 0 1.169 - 1.462: 1 Chirality restraints: 3922 Sorted by residual: chirality pdb=" CB THR A 37 " pdb=" CA THR A 37 " pdb=" OG1 THR A 37 " pdb=" CG2 THR A 37 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.34e+01 chirality pdb=" CA ASN C 821 " pdb=" N ASN C 821 " pdb=" C ASN C 821 " pdb=" CB ASN C 821 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CA THR B 115 " pdb=" N THR B 115 " pdb=" C THR B 115 " pdb=" CB THR B 115 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.89e+00 ... (remaining 3919 not shown) Planarity restraints: 7278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 70 " -0.294 2.00e-02 2.50e+03 3.06e-01 1.40e+03 pdb=" CG ASN C 70 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 70 " 0.280 2.00e-02 2.50e+03 pdb=" ND2 ASN C 70 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 70 " -0.453 2.00e-02 2.50e+03 pdb="HD22 ASN C 70 " 0.436 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 361 " -0.284 2.00e-02 2.50e+03 2.98e-01 1.33e+03 pdb=" CG ASN B 361 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN B 361 " 0.279 2.00e-02 2.50e+03 pdb=" ND2 ASN B 361 " 0.009 2.00e-02 2.50e+03 pdb="HD21 ASN B 361 " -0.443 2.00e-02 2.50e+03 pdb="HD22 ASN B 361 " 0.421 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 91 " -0.217 2.00e-02 2.50e+03 2.61e-01 1.02e+03 pdb=" CD GLN C 91 " -0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN C 91 " 0.220 2.00e-02 2.50e+03 pdb=" NE2 GLN C 91 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN C 91 " 0.397 2.00e-02 2.50e+03 pdb="HE22 GLN C 91 " -0.393 2.00e-02 2.50e+03 ... (remaining 7275 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 3512 2.20 - 2.80: 101823 2.80 - 3.40: 132947 3.40 - 4.00: 178862 4.00 - 4.60: 277303 Nonbonded interactions: 694447 Sorted by model distance: nonbonded pdb=" H GLN C 241 " pdb=" OE1 GLN C 245 " model vdw 1.603 1.850 nonbonded pdb=" OD1 ASP A 786 " pdb=" HZ3 LYS A 789 " model vdw 1.605 1.850 nonbonded pdb=" O MET A 478 " pdb=" HG SER A 481 " model vdw 1.612 1.850 nonbonded pdb=" OE1 GLU B 642 " pdb=" H GLU B 642 " model vdw 1.612 1.850 nonbonded pdb=" O ARG A 516 " pdb="HD22 ASN A 520 " model vdw 1.613 1.850 ... (remaining 694442 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 1046 or (resid 1101 and (name N or name C1 or na \ me C11 or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )))) selection = (chain 'B' and (resid 1 through 1046 or resid 1103)) selection = (chain 'C' and (resid 1 through 1046 or (resid 1103 and (name N or name C1 or na \ me C11 or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )))) } 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: 0.130 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: 0.770 Extract box with map and model: 3.360 Check model and map are aligned: 0.690 Set scattering table: 0.420 Process input model: 154.070 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.200 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.511 24744 Z= 0.832 Angle : 1.162 14.978 33594 Z= 0.707 Chirality : 0.073 1.462 3922 Planarity : 0.007 0.178 4281 Dihedral : 15.018 113.555 9079 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 1.93 % Allowed : 10.31 % Favored : 87.76 % Cbeta Deviations : 0.17 % 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: 0.36 (0.14), residues: 3136 helix: 1.13 (0.12), residues: 1682 sheet: -0.08 (0.24), residues: 419 loop : -1.02 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP C 864 HIS 0.012 0.002 HIS A1012 PHE 0.026 0.003 PHE B 611 TYR 0.025 0.004 TYR C 157 ARG 0.038 0.001 ARG B 781 *********************** 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 734 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 684 time to evaluate : 3.494 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 19 ILE cc_start: 0.7487 (mm) cc_final: 0.7272 (mt) REVERT: A 34 GLN cc_start: 0.7009 (tt0) cc_final: 0.6355 (tt0) REVERT: A 66 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 76 ARG cc_start: 0.7345 (mtm180) cc_final: 0.6974 (mtp85) REVERT: A 110 LYS cc_start: 0.8397 (mttm) cc_final: 0.8195 (mttm) REVERT: A 121 ASP cc_start: 0.7701 (m-30) cc_final: 0.7343 (m-30) REVERT: A 230 LEU cc_start: 0.6434 (pt) cc_final: 0.6227 (pp) REVERT: A 247 LYS cc_start: 0.8145 (mttt) cc_final: 0.7697 (mttm) REVERT: A 315 LYS cc_start: 0.7538 (mttt) cc_final: 0.7069 (mtmm) REVERT: A 365 THR cc_start: 0.7840 (m) cc_final: 0.7417 (p) REVERT: A 525 MET cc_start: 0.8065 (tmm) cc_final: 0.7782 (ttt) REVERT: A 663 SER cc_start: 0.6640 (m) cc_final: 0.6409 (p) REVERT: A 696 LYS cc_start: 0.7058 (mmmm) cc_final: 0.6829 (mmmm) REVERT: A 842 MET cc_start: 0.7028 (mtm) cc_final: 0.6794 (mtt) REVERT: A 892 CYS cc_start: 0.7288 (m) cc_final: 0.6004 (t) REVERT: A 911 PRO cc_start: 0.8255 (Cg_exo) cc_final: 0.8037 (Cg_endo) REVERT: A 975 THR cc_start: 0.7860 (m) cc_final: 0.7549 (p) REVERT: B 3 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7342 (mp10) REVERT: B 8 ARG cc_start: 0.7489 (mtt90) cc_final: 0.7223 (mtt-85) REVERT: B 20 MET cc_start: 0.6481 (mtt) cc_final: 0.6006 (mmm) REVERT: B 29 LYS cc_start: 0.7456 (mtpt) cc_final: 0.7112 (tptm) REVERT: B 35 TYR cc_start: 0.8089 (m-80) cc_final: 0.7885 (m-80) REVERT: B 42 THR cc_start: 0.8418 (p) cc_final: 0.7936 (m) REVERT: B 113 SER cc_start: 0.8904 (t) cc_final: 0.8472 (p) REVERT: B 115 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 148 ASN cc_start: 0.7792 (t0) cc_final: 0.7513 (t0) REVERT: B 174 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6499 (tt0) REVERT: B 212 SER cc_start: 0.8206 (m) cc_final: 0.7988 (t) REVERT: B 229 VAL cc_start: 0.8214 (p) cc_final: 0.7902 (t) REVERT: B 247 LYS cc_start: 0.6922 (mtpp) cc_final: 0.6430 (mttm) REVERT: B 248 ASN cc_start: 0.7030 (m-40) cc_final: 0.6605 (t0) REVERT: B 270 LEU cc_start: 0.7972 (mt) cc_final: 0.7769 (mt) REVERT: B 304 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6997 (mt-10) REVERT: B 308 GLN cc_start: 0.6813 (tt0) cc_final: 0.6487 (tp40) REVERT: B 310 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6909 (mt) REVERT: B 325 LEU cc_start: 0.8243 (mt) cc_final: 0.7908 (mm) REVERT: B 335 LEU cc_start: 0.7204 (mt) cc_final: 0.6976 (mp) REVERT: B 346 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6162 (tt0) REVERT: B 349 ILE cc_start: 0.8048 (mm) cc_final: 0.7838 (mm) REVERT: B 361 ASN cc_start: 0.8445 (p0) cc_final: 0.8184 (p0) REVERT: B 370 LEU cc_start: 0.8638 (mp) cc_final: 0.8417 (mm) REVERT: B 417 GLU cc_start: 0.7038 (tp30) cc_final: 0.6760 (mm-30) REVERT: B 422 GLU cc_start: 0.6695 (pt0) cc_final: 0.6313 (pt0) REVERT: B 429 THR cc_start: 0.8123 (m) cc_final: 0.7532 (p) REVERT: B 436 GLN cc_start: 0.7752 (tp40) cc_final: 0.7537 (mm110) REVERT: B 448 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8222 (t) REVERT: B 498 LYS cc_start: 0.7519 (tppt) cc_final: 0.6936 (mptm) REVERT: B 515 PHE cc_start: 0.6929 (m-80) cc_final: 0.6611 (m-80) REVERT: B 525 MET cc_start: 0.6147 (tpp) cc_final: 0.5753 (tpt) REVERT: B 666 MET cc_start: 0.5743 (mmt) cc_final: 0.5196 (tpp) REVERT: B 718 ARG cc_start: 0.7325 (ptt90) cc_final: 0.7042 (ppt-90) REVERT: B 723 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7087 (mm-30) REVERT: B 736 GLN cc_start: 0.6748 (tt0) cc_final: 0.6469 (tt0) REVERT: B 740 MET cc_start: 0.6118 (mmt) cc_final: 0.5823 (mmm) REVERT: B 783 MET cc_start: 0.7458 (mmm) cc_final: 0.7244 (mmm) REVERT: B 798 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6495 (mm-30) REVERT: B 809 GLU cc_start: 0.7661 (pt0) cc_final: 0.7420 (pt0) REVERT: B 828 ILE cc_start: 0.8260 (mt) cc_final: 0.7946 (mp) REVERT: B 884 LEU cc_start: 0.7792 (mt) cc_final: 0.7567 (mm) REVERT: B 928 LYS cc_start: 0.7245 (mtmt) cc_final: 0.7010 (mtmm) REVERT: B 967 LYS cc_start: 0.6885 (mmpt) cc_final: 0.6674 (mmmm) REVERT: B 977 HIS cc_start: 0.5973 (m-70) cc_final: 0.5613 (t-170) REVERT: B 980 LYS cc_start: 0.7582 (tttt) cc_final: 0.7076 (tmtm) REVERT: B 1002 LEU cc_start: 0.7712 (mt) cc_final: 0.7407 (mt) REVERT: C 20 MET cc_start: 0.8553 (mtp) cc_final: 0.8332 (mtp) REVERT: C 25 LEU cc_start: 0.8682 (mt) cc_final: 0.8435 (mt) REVERT: C 63 GLN cc_start: 0.7065 (mt0) cc_final: 0.6829 (mt0) REVERT: C 101 ASP cc_start: 0.8038 (m-30) cc_final: 0.7632 (m-30) REVERT: C 121 ASP cc_start: 0.6499 (m-30) cc_final: 0.5903 (t70) REVERT: C 124 ARG cc_start: 0.7075 (mtt-85) cc_final: 0.6840 (mtp85) REVERT: C 146 ASP cc_start: 0.7920 (m-30) cc_final: 0.7459 (m-30) REVERT: C 164 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6409 (mp0) REVERT: C 174 GLU cc_start: 0.7339 (tt0) cc_final: 0.7111 (tt0) REVERT: C 208 GLN cc_start: 0.7845 (mt0) cc_final: 0.7592 (mm-40) REVERT: C 238 SER cc_start: 0.7592 (p) cc_final: 0.7168 (m) REVERT: C 417 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6719 (mm-30) REVERT: C 445 ILE cc_start: 0.8179 (mt) cc_final: 0.7903 (mm) REVERT: C 498 LYS cc_start: 0.8018 (mttt) cc_final: 0.7756 (mmtm) REVERT: C 545 VAL cc_start: 0.8254 (t) cc_final: 0.8003 (m) REVERT: C 560 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7301 (mmmm) REVERT: C 591 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7346 (mmtt) REVERT: C 601 MET cc_start: 0.8558 (mtp) cc_final: 0.8264 (mtm) REVERT: C 602 ASN cc_start: 0.7543 (m110) cc_final: 0.7265 (m-40) REVERT: C 604 LYS cc_start: 0.7513 (mttp) cc_final: 0.7292 (mtpm) REVERT: C 631 LYS cc_start: 0.8616 (tttp) cc_final: 0.8341 (tttm) REVERT: C 657 MET cc_start: 0.6745 (mmm) cc_final: 0.6330 (mmm) REVERT: C 661 ASP cc_start: 0.7271 (m-30) cc_final: 0.5933 (t0) REVERT: C 722 GLN cc_start: 0.7416 (mt0) cc_final: 0.5942 (mm-40) REVERT: C 751 MET cc_start: 0.8304 (mmm) cc_final: 0.7888 (mmm) REVERT: C 962 LYS cc_start: 0.7498 (tttm) cc_final: 0.7175 (tttp) REVERT: C 984 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7814 (ttt180) REVERT: C 987 ILE cc_start: 0.8045 (mt) cc_final: 0.7759 (mm) outliers start: 50 outliers final: 27 residues processed: 720 average time/residue: 1.9641 time to fit residues: 1742.1096 Evaluate side-chains 642 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 611 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 811 THR Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 909 VAL 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: 0.9980 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 283 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 669 GLN B 106 GLN ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 241 GLN C 877 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24744 Z= 0.175 Angle : 0.585 11.462 33594 Z= 0.312 Chirality : 0.047 1.414 3922 Planarity : 0.005 0.053 4281 Dihedral : 9.834 91.579 3666 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 2.70 % Allowed : 15.71 % Favored : 81.58 % 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: 0.99 (0.15), residues: 3136 helix: 1.65 (0.12), residues: 1673 sheet: 0.15 (0.24), residues: 426 loop : -0.72 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 635 HIS 0.003 0.001 HIS B 500 PHE 0.011 0.001 PHE B 682 TYR 0.011 0.001 TYR B 664 ARG 0.007 0.000 ARG B 433 *********************** 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 703 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 633 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7414 (mm) cc_final: 0.7126 (mt) REVERT: A 76 ARG cc_start: 0.7283 (mtm180) cc_final: 0.6969 (mtp85) REVERT: A 110 LYS cc_start: 0.8376 (mttm) cc_final: 0.8144 (mttm) REVERT: A 121 ASP cc_start: 0.7492 (m-30) cc_final: 0.7151 (m-30) REVERT: A 247 LYS cc_start: 0.8017 (mttt) cc_final: 0.7573 (mttm) REVERT: A 315 LYS cc_start: 0.7498 (mttt) cc_final: 0.7192 (mttp) REVERT: A 365 THR cc_start: 0.7833 (m) cc_final: 0.7449 (p) REVERT: A 400 LEU cc_start: 0.7346 (mt) cc_final: 0.7062 (mt) REVERT: A 525 MET cc_start: 0.7917 (tmm) cc_final: 0.7707 (ttt) REVERT: A 684 LEU cc_start: 0.6964 (tp) cc_final: 0.6715 (tm) REVERT: A 696 LYS cc_start: 0.7094 (mmmm) cc_final: 0.6848 (mmmm) REVERT: A 818 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7420 (mm-30) REVERT: A 890 PHE cc_start: 0.7565 (t80) cc_final: 0.7152 (t80) REVERT: A 892 CYS cc_start: 0.7347 (m) cc_final: 0.6137 (t) REVERT: A 956 LEU cc_start: 0.7072 (mt) cc_final: 0.6841 (tp) REVERT: A 975 THR cc_start: 0.7862 (m) cc_final: 0.7534 (p) REVERT: B 3 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7324 (mp10) REVERT: B 8 ARG cc_start: 0.7351 (mtt90) cc_final: 0.7095 (mtt-85) REVERT: B 20 MET cc_start: 0.6401 (mtt) cc_final: 0.5932 (mmm) REVERT: B 21 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7499 (tt) REVERT: B 29 LYS cc_start: 0.7365 (mtpt) cc_final: 0.6971 (tptp) REVERT: B 42 THR cc_start: 0.8362 (p) cc_final: 0.7933 (m) REVERT: B 55 GLU cc_start: 0.7172 (tt0) cc_final: 0.6753 (tp30) REVERT: B 113 SER cc_start: 0.8517 (t) cc_final: 0.8151 (p) REVERT: B 148 ASN cc_start: 0.7952 (t0) cc_final: 0.7693 (t0) REVERT: B 174 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6358 (tt0) REVERT: B 229 VAL cc_start: 0.8198 (p) cc_final: 0.7883 (t) REVERT: B 247 LYS cc_start: 0.6902 (mtpp) cc_final: 0.6358 (mttm) REVERT: B 269 GLU cc_start: 0.7632 (tt0) cc_final: 0.7007 (tt0) REVERT: B 308 GLN cc_start: 0.6694 (tt0) cc_final: 0.6146 (tp-100) REVERT: B 309 ARG cc_start: 0.6535 (tpt90) cc_final: 0.6326 (mmm160) REVERT: B 325 LEU cc_start: 0.8190 (mt) cc_final: 0.7883 (mm) REVERT: B 334 ARG cc_start: 0.6878 (mtt-85) cc_final: 0.6594 (mtt90) REVERT: B 335 LEU cc_start: 0.7149 (mt) cc_final: 0.6881 (mp) REVERT: B 346 GLU cc_start: 0.6409 (mt-10) cc_final: 0.6110 (tt0) REVERT: B 417 GLU cc_start: 0.7156 (tp30) cc_final: 0.6763 (mm-30) REVERT: B 429 THR cc_start: 0.8179 (m) cc_final: 0.7577 (p) REVERT: B 436 GLN cc_start: 0.7757 (tp40) cc_final: 0.7549 (mm110) REVERT: B 498 LYS cc_start: 0.7340 (tppt) cc_final: 0.6937 (mptm) REVERT: B 525 MET cc_start: 0.6179 (tpp) cc_final: 0.5850 (tpt) REVERT: B 553 LEU cc_start: 0.7895 (tp) cc_final: 0.7537 (tm) REVERT: B 579 GLN cc_start: 0.5945 (OUTLIER) cc_final: 0.5444 (mm-40) REVERT: B 637 LYS cc_start: 0.5832 (tppt) cc_final: 0.5624 (mtpp) REVERT: B 666 MET cc_start: 0.5737 (mmt) cc_final: 0.5265 (tpp) REVERT: B 718 ARG cc_start: 0.7225 (ptt90) cc_final: 0.6904 (ppt-90) REVERT: B 736 GLN cc_start: 0.6780 (tt0) cc_final: 0.6517 (tt0) REVERT: B 768 ARG cc_start: 0.5679 (mtp85) cc_final: 0.5296 (mpt-90) REVERT: B 788 ASN cc_start: 0.7643 (m-40) cc_final: 0.7373 (m-40) REVERT: B 798 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6433 (mm-30) REVERT: B 809 GLU cc_start: 0.7456 (pt0) cc_final: 0.7254 (pt0) REVERT: B 928 LYS cc_start: 0.7335 (mtmt) cc_final: 0.7083 (mtmm) REVERT: B 947 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7442 (mm) REVERT: B 967 LYS cc_start: 0.7024 (mmpt) cc_final: 0.6760 (mmmm) REVERT: B 977 HIS cc_start: 0.5996 (m-70) cc_final: 0.5749 (t-170) REVERT: B 980 LYS cc_start: 0.7551 (tttt) cc_final: 0.7042 (tmtm) REVERT: B 1002 LEU cc_start: 0.7889 (mt) cc_final: 0.7612 (mt) REVERT: C 20 MET cc_start: 0.8428 (mtp) cc_final: 0.8143 (mtp) REVERT: C 25 LEU cc_start: 0.8489 (mt) cc_final: 0.8197 (mt) REVERT: C 63 GLN cc_start: 0.7128 (mt0) cc_final: 0.6835 (mt0) REVERT: C 95 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6479 (mt-10) REVERT: C 101 ASP cc_start: 0.8010 (m-30) cc_final: 0.7624 (m-30) REVERT: C 120 GLU cc_start: 0.6920 (tt0) cc_final: 0.6519 (tt0) REVERT: C 121 ASP cc_start: 0.6245 (m-30) cc_final: 0.5650 (t70) REVERT: C 123 GLN cc_start: 0.8097 (mt0) cc_final: 0.7582 (mt0) REVERT: C 124 ARG cc_start: 0.7033 (mtt-85) cc_final: 0.6762 (mtp85) REVERT: C 146 ASP cc_start: 0.7858 (m-30) cc_final: 0.7337 (m-30) REVERT: C 174 GLU cc_start: 0.7314 (tt0) cc_final: 0.7052 (tt0) REVERT: C 208 GLN cc_start: 0.7759 (mt0) cc_final: 0.7498 (mm110) REVERT: C 238 SER cc_start: 0.7568 (p) cc_final: 0.7145 (m) REVERT: C 241 GLN cc_start: 0.7421 (mt0) cc_final: 0.7111 (mt0) REVERT: C 417 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6418 (mm-30) REVERT: C 445 ILE cc_start: 0.8057 (mt) cc_final: 0.7833 (mm) REVERT: C 545 VAL cc_start: 0.8202 (t) cc_final: 0.7977 (m) REVERT: C 560 LYS cc_start: 0.7595 (mmtt) cc_final: 0.7159 (mmmm) REVERT: C 591 LYS cc_start: 0.7671 (mtpt) cc_final: 0.7239 (mmtt) REVERT: C 602 ASN cc_start: 0.7451 (m110) cc_final: 0.7165 (m-40) REVERT: C 604 LYS cc_start: 0.7406 (mttp) cc_final: 0.7119 (mtpm) REVERT: C 608 GLU cc_start: 0.7362 (tp30) cc_final: 0.6994 (mm-30) REVERT: C 631 LYS cc_start: 0.8468 (tttp) cc_final: 0.8185 (tttm) REVERT: C 657 MET cc_start: 0.6631 (mmm) cc_final: 0.6254 (mmm) REVERT: C 661 ASP cc_start: 0.7277 (m-30) cc_final: 0.5896 (t0) REVERT: C 722 GLN cc_start: 0.7293 (mt0) cc_final: 0.5926 (mm-40) REVERT: C 768 ARG cc_start: 0.8350 (mtp85) cc_final: 0.7814 (ttt-90) REVERT: C 771 LYS cc_start: 0.8278 (mttp) cc_final: 0.7988 (mttm) REVERT: C 780 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8479 (p) REVERT: C 796 LYS cc_start: 0.6549 (mmmm) cc_final: 0.6275 (mmtp) REVERT: C 871 GLU cc_start: 0.7971 (tt0) cc_final: 0.7556 (tt0) REVERT: C 873 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7199 (mt-10) REVERT: C 962 LYS cc_start: 0.7434 (tttm) cc_final: 0.7204 (tttp) REVERT: C 984 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7405 (ttt180) REVERT: C 987 ILE cc_start: 0.7875 (mt) cc_final: 0.7594 (mm) outliers start: 70 outliers final: 40 residues processed: 674 average time/residue: 2.1144 time to fit residues: 1753.4783 Evaluate side-chains 657 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 613 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 909 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 8.9990 chunk 87 optimal weight: 50.0000 chunk 235 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 283 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 112 GLN B 210 GLN B 519 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24744 Z= 0.310 Angle : 0.600 11.397 33594 Z= 0.319 Chirality : 0.048 1.442 3922 Planarity : 0.005 0.050 4281 Dihedral : 9.194 88.271 3639 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.44 % Allowed : 16.56 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3136 helix: 1.54 (0.12), residues: 1672 sheet: 0.13 (0.24), residues: 441 loop : -0.79 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 635 HIS 0.005 0.001 HIS B 424 PHE 0.017 0.002 PHE C 682 TYR 0.016 0.002 TYR C 897 ARG 0.004 0.000 ARG C 872 *********************** 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 700 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 611 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7426 (mm) cc_final: 0.7223 (mt) REVERT: A 66 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 76 ARG cc_start: 0.7301 (mtm180) cc_final: 0.6991 (mtp85) REVERT: A 110 LYS cc_start: 0.8342 (mttm) cc_final: 0.8126 (mttm) REVERT: A 121 ASP cc_start: 0.7607 (m-30) cc_final: 0.7239 (m-30) REVERT: A 153 ASP cc_start: 0.7425 (m-30) cc_final: 0.7166 (m-30) REVERT: A 164 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: A 247 LYS cc_start: 0.8041 (mttt) cc_final: 0.7583 (mttm) REVERT: A 315 LYS cc_start: 0.7508 (mttt) cc_final: 0.7204 (mttp) REVERT: A 337 ILE cc_start: 0.6985 (mm) cc_final: 0.6650 (mm) REVERT: A 340 VAL cc_start: 0.7186 (t) cc_final: 0.6875 (p) REVERT: A 400 LEU cc_start: 0.7343 (mt) cc_final: 0.7061 (mt) REVERT: A 525 MET cc_start: 0.7929 (tmm) cc_final: 0.7729 (ttt) REVERT: A 684 LEU cc_start: 0.6997 (tp) cc_final: 0.6770 (tm) REVERT: A 696 LYS cc_start: 0.7099 (mmmm) cc_final: 0.6845 (mmmm) REVERT: A 818 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7442 (mm-30) REVERT: A 890 PHE cc_start: 0.7563 (t80) cc_final: 0.7160 (t80) REVERT: A 892 CYS cc_start: 0.7366 (m) cc_final: 0.6138 (t) REVERT: A 956 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6999 (tp) REVERT: A 975 THR cc_start: 0.7863 (m) cc_final: 0.7549 (p) REVERT: B 3 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7374 (mp10) REVERT: B 8 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7181 (mtt-85) REVERT: B 20 MET cc_start: 0.6554 (mtt) cc_final: 0.5978 (mmm) REVERT: B 21 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7488 (tp) REVERT: B 29 LYS cc_start: 0.7347 (mtpt) cc_final: 0.6978 (tptm) REVERT: B 42 THR cc_start: 0.8392 (p) cc_final: 0.7949 (m) REVERT: B 55 GLU cc_start: 0.7170 (tt0) cc_final: 0.6723 (tp30) REVERT: B 113 SER cc_start: 0.8578 (t) cc_final: 0.8262 (p) REVERT: B 148 ASN cc_start: 0.7951 (t0) cc_final: 0.7701 (t0) REVERT: B 155 LYS cc_start: 0.5392 (mttt) cc_final: 0.5157 (ttmt) REVERT: B 174 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6345 (tt0) REVERT: B 229 VAL cc_start: 0.8211 (p) cc_final: 0.7909 (t) REVERT: B 247 LYS cc_start: 0.6962 (mtpp) cc_final: 0.6426 (mttm) REVERT: B 289 LEU cc_start: 0.7757 (tt) cc_final: 0.7486 (tp) REVERT: B 308 GLN cc_start: 0.6665 (tt0) cc_final: 0.6071 (tp-100) REVERT: B 309 ARG cc_start: 0.6476 (tpt90) cc_final: 0.6073 (mmm160) REVERT: B 325 LEU cc_start: 0.8208 (mt) cc_final: 0.7893 (mm) REVERT: B 346 GLU cc_start: 0.6444 (mt-10) cc_final: 0.6197 (tt0) REVERT: B 417 GLU cc_start: 0.7154 (tp30) cc_final: 0.6802 (mm-30) REVERT: B 429 THR cc_start: 0.8129 (m) cc_final: 0.7526 (p) REVERT: B 448 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8174 (t) REVERT: B 498 LYS cc_start: 0.7404 (tppt) cc_final: 0.6952 (mptm) REVERT: B 525 MET cc_start: 0.6206 (tpp) cc_final: 0.5848 (tpt) REVERT: B 553 LEU cc_start: 0.7868 (tp) cc_final: 0.7510 (tm) REVERT: B 579 GLN cc_start: 0.5860 (OUTLIER) cc_final: 0.5425 (tp-100) REVERT: B 637 LYS cc_start: 0.5719 (tppt) cc_final: 0.5452 (mtpp) REVERT: B 666 MET cc_start: 0.5733 (mmt) cc_final: 0.5223 (tpp) REVERT: B 692 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.5767 (mt0) REVERT: B 718 ARG cc_start: 0.7350 (ptt90) cc_final: 0.7111 (ppt-90) REVERT: B 736 GLN cc_start: 0.6815 (tt0) cc_final: 0.6589 (tt0) REVERT: B 782 MET cc_start: 0.7616 (mmp) cc_final: 0.7229 (mmp) REVERT: B 788 ASN cc_start: 0.7703 (m-40) cc_final: 0.7405 (m-40) REVERT: B 798 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6419 (mm-30) REVERT: B 809 GLU cc_start: 0.7472 (pt0) cc_final: 0.7260 (pt0) REVERT: B 828 ILE cc_start: 0.8282 (mt) cc_final: 0.7949 (mp) REVERT: B 928 LYS cc_start: 0.7204 (mtmt) cc_final: 0.6913 (mtmm) REVERT: B 967 LYS cc_start: 0.7141 (mmpt) cc_final: 0.6868 (mmmm) REVERT: B 977 HIS cc_start: 0.6000 (m-70) cc_final: 0.5671 (t-170) REVERT: B 980 LYS cc_start: 0.7670 (tttt) cc_final: 0.7118 (tmtm) REVERT: B 1002 LEU cc_start: 0.7894 (mt) cc_final: 0.7660 (mt) REVERT: B 1027 PHE cc_start: 0.7434 (m-80) cc_final: 0.7130 (m-10) REVERT: C 20 MET cc_start: 0.8407 (mtp) cc_final: 0.8169 (mtp) REVERT: C 25 LEU cc_start: 0.8507 (mt) cc_final: 0.8228 (mt) REVERT: C 63 GLN cc_start: 0.7094 (mt0) cc_final: 0.6821 (mt0) REVERT: C 91 GLN cc_start: 0.8620 (tt0) cc_final: 0.8407 (tt0) REVERT: C 95 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6518 (mt-10) REVERT: C 101 ASP cc_start: 0.8012 (m-30) cc_final: 0.7617 (m-30) REVERT: C 124 ARG cc_start: 0.7033 (mtt-85) cc_final: 0.6797 (mtp85) REVERT: C 146 ASP cc_start: 0.7856 (m-30) cc_final: 0.7349 (m-30) REVERT: C 208 GLN cc_start: 0.7839 (mt0) cc_final: 0.7572 (mm110) REVERT: C 238 SER cc_start: 0.7564 (p) cc_final: 0.7130 (m) REVERT: C 417 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6527 (mm-30) REVERT: C 445 ILE cc_start: 0.8141 (mt) cc_final: 0.7845 (mm) REVERT: C 560 LYS cc_start: 0.7638 (mmtt) cc_final: 0.7189 (mmmm) REVERT: C 591 LYS cc_start: 0.7705 (mtpt) cc_final: 0.7238 (mmtt) REVERT: C 602 ASN cc_start: 0.7511 (m110) cc_final: 0.7213 (m-40) REVERT: C 604 LYS cc_start: 0.7530 (mttp) cc_final: 0.7250 (mtpm) REVERT: C 631 LYS cc_start: 0.8505 (tttp) cc_final: 0.8229 (tttm) REVERT: C 657 MET cc_start: 0.6648 (mmm) cc_final: 0.6270 (mmm) REVERT: C 661 ASP cc_start: 0.7211 (m-30) cc_final: 0.5879 (t0) REVERT: C 768 ARG cc_start: 0.8365 (mtp85) cc_final: 0.7908 (ttt-90) REVERT: C 771 LYS cc_start: 0.8246 (mttp) cc_final: 0.7973 (mttm) REVERT: C 873 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7286 (mt-10) REVERT: C 962 LYS cc_start: 0.7475 (tttm) cc_final: 0.7234 (tttp) REVERT: C 981 MET cc_start: 0.6451 (ttm) cc_final: 0.6196 (ttm) REVERT: C 984 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7460 (ttt180) REVERT: C 987 ILE cc_start: 0.7958 (mt) cc_final: 0.7686 (mm) outliers start: 89 outliers final: 54 residues processed: 659 average time/residue: 2.1440 time to fit residues: 1742.7464 Evaluate side-chains 660 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 600 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 601 MET Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 926 ILE Chi-restraints excluded: chain C residue 990 THR Chi-restraints excluded: chain C residue 1004 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 269 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 210 GLN ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 241 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24744 Z= 0.284 Angle : 0.582 11.401 33594 Z= 0.309 Chirality : 0.047 1.433 3922 Planarity : 0.005 0.052 4281 Dihedral : 8.697 88.307 3633 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.24 % Allowed : 17.95 % Favored : 78.80 % 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: 0.89 (0.15), residues: 3136 helix: 1.56 (0.12), residues: 1678 sheet: 0.17 (0.24), residues: 439 loop : -0.82 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 635 HIS 0.004 0.001 HIS B 424 PHE 0.066 0.002 PHE A1032 TYR 0.015 0.002 TYR C 897 ARG 0.004 0.000 ARG C 433 *********************** 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 691 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 607 time to evaluate : 3.727 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 19 ILE cc_start: 0.7373 (mm) cc_final: 0.7170 (mt) REVERT: A 66 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7917 (mt-10) REVERT: A 76 ARG cc_start: 0.7299 (mtm180) cc_final: 0.6998 (mtp85) REVERT: A 110 LYS cc_start: 0.8341 (mttm) cc_final: 0.8127 (mttm) REVERT: A 121 ASP cc_start: 0.7591 (m-30) cc_final: 0.7221 (m-30) REVERT: A 153 ASP cc_start: 0.7425 (m-30) cc_final: 0.7157 (m-30) REVERT: A 164 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: A 226 GLN cc_start: 0.6372 (mt0) cc_final: 0.6074 (mm-40) REVERT: A 247 LYS cc_start: 0.8050 (mttt) cc_final: 0.7592 (mttm) REVERT: A 315 LYS cc_start: 0.7511 (mttt) cc_final: 0.7170 (mttp) REVERT: A 337 ILE cc_start: 0.6973 (mm) cc_final: 0.6646 (mm) REVERT: A 340 VAL cc_start: 0.7149 (t) cc_final: 0.6839 (p) REVERT: A 355 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6993 (tpp) REVERT: A 400 LEU cc_start: 0.7276 (mt) cc_final: 0.6987 (mt) REVERT: A 684 LEU cc_start: 0.6989 (tp) cc_final: 0.6730 (tm) REVERT: A 696 LYS cc_start: 0.7097 (mmmm) cc_final: 0.6841 (mmmm) REVERT: A 818 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7341 (mm-30) REVERT: A 890 PHE cc_start: 0.7559 (t80) cc_final: 0.7138 (t80) REVERT: A 892 CYS cc_start: 0.7347 (m) cc_final: 0.6159 (t) REVERT: A 975 THR cc_start: 0.7850 (m) cc_final: 0.7529 (p) REVERT: B 3 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7353 (mp10) REVERT: B 8 ARG cc_start: 0.7458 (mtt90) cc_final: 0.7170 (mtt-85) REVERT: B 20 MET cc_start: 0.6561 (mtt) cc_final: 0.5994 (mmm) REVERT: B 21 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7498 (tt) REVERT: B 29 LYS cc_start: 0.7342 (mtpt) cc_final: 0.6942 (tptp) REVERT: B 42 THR cc_start: 0.8397 (p) cc_final: 0.7958 (m) REVERT: B 55 GLU cc_start: 0.7286 (tt0) cc_final: 0.6810 (tp30) REVERT: B 113 SER cc_start: 0.8600 (t) cc_final: 0.8281 (p) REVERT: B 148 ASN cc_start: 0.7895 (t0) cc_final: 0.7662 (t0) REVERT: B 174 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6384 (tt0) REVERT: B 208 GLN cc_start: 0.7277 (mt0) cc_final: 0.6772 (mm-40) REVERT: B 229 VAL cc_start: 0.8213 (p) cc_final: 0.7903 (t) REVERT: B 247 LYS cc_start: 0.6961 (mtpp) cc_final: 0.6417 (mttm) REVERT: B 308 GLN cc_start: 0.6626 (tt0) cc_final: 0.6014 (tp-100) REVERT: B 309 ARG cc_start: 0.6519 (tpt90) cc_final: 0.6091 (mmm160) REVERT: B 325 LEU cc_start: 0.8208 (mt) cc_final: 0.7884 (mm) REVERT: B 335 LEU cc_start: 0.7058 (mt) cc_final: 0.6764 (mp) REVERT: B 346 GLU cc_start: 0.6392 (mt-10) cc_final: 0.6137 (tt0) REVERT: B 417 GLU cc_start: 0.7157 (tp30) cc_final: 0.6761 (mm-30) REVERT: B 429 THR cc_start: 0.8115 (m) cc_final: 0.7515 (p) REVERT: B 448 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8118 (t) REVERT: B 498 LYS cc_start: 0.7422 (tppt) cc_final: 0.6931 (mptm) REVERT: B 553 LEU cc_start: 0.7808 (tp) cc_final: 0.7458 (tm) REVERT: B 579 GLN cc_start: 0.5700 (OUTLIER) cc_final: 0.5323 (tp-100) REVERT: B 637 LYS cc_start: 0.5806 (tppt) cc_final: 0.5443 (mtpm) REVERT: B 666 MET cc_start: 0.5731 (mmt) cc_final: 0.5269 (tpp) REVERT: B 692 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.5766 (mt0) REVERT: B 718 ARG cc_start: 0.7290 (ptt90) cc_final: 0.7049 (ppt-90) REVERT: B 768 ARG cc_start: 0.5671 (mtp85) cc_final: 0.5278 (mpt-90) REVERT: B 782 MET cc_start: 0.7605 (mmp) cc_final: 0.7286 (mmp) REVERT: B 788 ASN cc_start: 0.7709 (m-40) cc_final: 0.7410 (m-40) REVERT: B 798 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6387 (mm-30) REVERT: B 807 THR cc_start: 0.7140 (OUTLIER) cc_final: 0.6684 (t) REVERT: B 928 LYS cc_start: 0.7181 (mtmt) cc_final: 0.6884 (mtmm) REVERT: B 967 LYS cc_start: 0.6979 (mmpt) cc_final: 0.6650 (mmmm) REVERT: B 977 HIS cc_start: 0.5969 (m-70) cc_final: 0.5673 (t-170) REVERT: B 980 LYS cc_start: 0.7691 (tttt) cc_final: 0.7149 (tmtm) REVERT: B 1002 LEU cc_start: 0.7865 (mt) cc_final: 0.7655 (mt) REVERT: B 1027 PHE cc_start: 0.7390 (m-80) cc_final: 0.7121 (m-10) REVERT: C 20 MET cc_start: 0.8392 (mtp) cc_final: 0.8153 (mtp) REVERT: C 25 LEU cc_start: 0.8491 (mt) cc_final: 0.8209 (mt) REVERT: C 63 GLN cc_start: 0.7083 (mt0) cc_final: 0.6831 (mt0) REVERT: C 91 GLN cc_start: 0.8591 (tt0) cc_final: 0.8373 (tt0) REVERT: C 95 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6520 (mt-10) REVERT: C 101 ASP cc_start: 0.7998 (m-30) cc_final: 0.7612 (m-30) REVERT: C 124 ARG cc_start: 0.7056 (mtt-85) cc_final: 0.6796 (mtp85) REVERT: C 146 ASP cc_start: 0.7820 (m-30) cc_final: 0.7279 (m-30) REVERT: C 208 GLN cc_start: 0.7816 (mt0) cc_final: 0.7609 (mm110) REVERT: C 238 SER cc_start: 0.7560 (p) cc_final: 0.7122 (m) REVERT: C 248 ASN cc_start: 0.7361 (OUTLIER) cc_final: 0.6681 (m-40) REVERT: C 417 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6538 (mm-30) REVERT: C 445 ILE cc_start: 0.8075 (mt) cc_final: 0.7845 (mm) REVERT: C 560 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7130 (mmmm) REVERT: C 591 LYS cc_start: 0.7704 (mtpt) cc_final: 0.7277 (mmtt) REVERT: C 602 ASN cc_start: 0.7475 (m110) cc_final: 0.7230 (m-40) REVERT: C 604 LYS cc_start: 0.7397 (mttp) cc_final: 0.7112 (mtpm) REVERT: C 631 LYS cc_start: 0.8468 (tttp) cc_final: 0.8193 (tttm) REVERT: C 657 MET cc_start: 0.6645 (mmm) cc_final: 0.6263 (mmm) REVERT: C 661 ASP cc_start: 0.7208 (m-30) cc_final: 0.5892 (t0) REVERT: C 768 ARG cc_start: 0.8384 (mtp85) cc_final: 0.7914 (ttt-90) REVERT: C 771 LYS cc_start: 0.8201 (mttp) cc_final: 0.7897 (mttm) REVERT: C 871 GLU cc_start: 0.7956 (tt0) cc_final: 0.7504 (tt0) REVERT: C 873 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7251 (mt-10) REVERT: C 962 LYS cc_start: 0.7527 (tttm) cc_final: 0.7294 (tttp) REVERT: C 984 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7446 (ttt180) REVERT: C 987 ILE cc_start: 0.7939 (mt) cc_final: 0.7676 (mm) outliers start: 84 outliers final: 59 residues processed: 652 average time/residue: 2.0083 time to fit residues: 1604.5738 Evaluate side-chains 664 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 597 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 601 MET Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 926 ILE Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 990 THR Chi-restraints excluded: chain C residue 1004 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24744 Z= 0.231 Angle : 0.552 11.379 33594 Z= 0.289 Chirality : 0.046 1.425 3922 Planarity : 0.005 0.050 4281 Dihedral : 8.248 83.573 3630 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.13 % Allowed : 17.99 % Favored : 78.88 % 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: 1.05 (0.15), residues: 3136 helix: 1.73 (0.13), residues: 1675 sheet: 0.16 (0.24), residues: 445 loop : -0.76 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 635 HIS 0.003 0.001 HIS A1012 PHE 0.020 0.001 PHE A1032 TYR 0.013 0.001 TYR C 897 ARG 0.006 0.000 ARG A 982 *********************** 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 684 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 603 time to evaluate : 4.577 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 19 ILE cc_start: 0.7371 (mm) cc_final: 0.7168 (mt) REVERT: A 66 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7792 (tt0) REVERT: A 76 ARG cc_start: 0.7295 (mtm180) cc_final: 0.7015 (mtp85) REVERT: A 110 LYS cc_start: 0.8332 (mttm) cc_final: 0.8128 (mttm) REVERT: A 121 ASP cc_start: 0.7500 (m-30) cc_final: 0.7138 (m-30) REVERT: A 153 ASP cc_start: 0.7373 (m-30) cc_final: 0.7086 (m-30) REVERT: A 164 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: A 226 GLN cc_start: 0.6410 (mt0) cc_final: 0.6121 (mm-40) REVERT: A 247 LYS cc_start: 0.8066 (mttt) cc_final: 0.7612 (mttm) REVERT: A 315 LYS cc_start: 0.7511 (mttt) cc_final: 0.7175 (mttp) REVERT: A 328 ASP cc_start: 0.7106 (t0) cc_final: 0.6868 (t0) REVERT: A 340 VAL cc_start: 0.7143 (t) cc_final: 0.6830 (p) REVERT: A 355 MET cc_start: 0.7214 (tpp) cc_final: 0.6833 (tpp) REVERT: A 400 LEU cc_start: 0.7252 (mt) cc_final: 0.6925 (mt) REVERT: A 608 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.6030 (tt0) REVERT: A 684 LEU cc_start: 0.6989 (tp) cc_final: 0.6742 (tm) REVERT: A 696 LYS cc_start: 0.6992 (mmmm) cc_final: 0.6734 (mmmm) REVERT: A 818 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7340 (mm-30) REVERT: A 892 CYS cc_start: 0.7336 (m) cc_final: 0.6161 (t) REVERT: A 975 THR cc_start: 0.7833 (m) cc_final: 0.7545 (p) REVERT: A 988 MET cc_start: 0.6949 (ttm) cc_final: 0.6748 (ttm) REVERT: B 3 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7385 (mp10) REVERT: B 8 ARG cc_start: 0.7424 (mtt90) cc_final: 0.7111 (mtt-85) REVERT: B 20 MET cc_start: 0.6554 (mtt) cc_final: 0.5986 (mmm) REVERT: B 21 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7524 (tt) REVERT: B 29 LYS cc_start: 0.7370 (mtpt) cc_final: 0.7013 (tptm) REVERT: B 42 THR cc_start: 0.8396 (p) cc_final: 0.7961 (m) REVERT: B 55 GLU cc_start: 0.7340 (tt0) cc_final: 0.6865 (tp30) REVERT: B 113 SER cc_start: 0.8567 (t) cc_final: 0.8250 (p) REVERT: B 115 THR cc_start: 0.8293 (p) cc_final: 0.8060 (t) REVERT: B 148 ASN cc_start: 0.7903 (t0) cc_final: 0.7690 (t0) REVERT: B 174 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6366 (tt0) REVERT: B 208 GLN cc_start: 0.7260 (mt0) cc_final: 0.6811 (mm-40) REVERT: B 229 VAL cc_start: 0.8202 (p) cc_final: 0.7889 (t) REVERT: B 247 LYS cc_start: 0.6953 (mtpp) cc_final: 0.6400 (mttm) REVERT: B 289 LEU cc_start: 0.7877 (tt) cc_final: 0.7621 (tp) REVERT: B 308 GLN cc_start: 0.6611 (tt0) cc_final: 0.5987 (tp-100) REVERT: B 325 LEU cc_start: 0.8212 (mt) cc_final: 0.7880 (mm) REVERT: B 335 LEU cc_start: 0.7026 (mt) cc_final: 0.6750 (mp) REVERT: B 346 GLU cc_start: 0.6384 (mt-10) cc_final: 0.6124 (tt0) REVERT: B 417 GLU cc_start: 0.7192 (tp30) cc_final: 0.6769 (mm-30) REVERT: B 429 THR cc_start: 0.8097 (m) cc_final: 0.7511 (p) REVERT: B 448 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8182 (t) REVERT: B 498 LYS cc_start: 0.7366 (tppt) cc_final: 0.6905 (mptm) REVERT: B 525 MET cc_start: 0.6328 (tpp) cc_final: 0.5981 (tpt) REVERT: B 536 MET cc_start: 0.6679 (mmt) cc_final: 0.6114 (mmt) REVERT: B 553 LEU cc_start: 0.7800 (tp) cc_final: 0.7443 (tm) REVERT: B 579 GLN cc_start: 0.5700 (OUTLIER) cc_final: 0.5332 (tp-100) REVERT: B 637 LYS cc_start: 0.5808 (tppt) cc_final: 0.5434 (mtpm) REVERT: B 666 MET cc_start: 0.5674 (mmt) cc_final: 0.5203 (tpp) REVERT: B 692 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.5733 (mt0) REVERT: B 718 ARG cc_start: 0.7234 (ptt90) cc_final: 0.6988 (ppt-90) REVERT: B 768 ARG cc_start: 0.5659 (mtp85) cc_final: 0.5257 (mpt-90) REVERT: B 782 MET cc_start: 0.7584 (mmp) cc_final: 0.7270 (mmp) REVERT: B 788 ASN cc_start: 0.7729 (m-40) cc_final: 0.7414 (m-40) REVERT: B 798 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6404 (mm-30) REVERT: B 807 THR cc_start: 0.7100 (OUTLIER) cc_final: 0.6681 (t) REVERT: B 928 LYS cc_start: 0.7298 (mtmt) cc_final: 0.7000 (mtmm) REVERT: B 947 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7650 (mm) REVERT: B 949 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7468 (tt) REVERT: B 967 LYS cc_start: 0.7003 (mmpt) cc_final: 0.6709 (mmmm) REVERT: B 977 HIS cc_start: 0.5982 (m-70) cc_final: 0.5678 (t-170) REVERT: B 980 LYS cc_start: 0.7606 (tttt) cc_final: 0.7066 (tmtm) REVERT: B 1027 PHE cc_start: 0.7287 (m-80) cc_final: 0.7060 (m-10) REVERT: C 20 MET cc_start: 0.8370 (mtp) cc_final: 0.8170 (mtp) REVERT: C 25 LEU cc_start: 0.8480 (mt) cc_final: 0.8208 (mt) REVERT: C 63 GLN cc_start: 0.7074 (mt0) cc_final: 0.6764 (mt0) REVERT: C 91 GLN cc_start: 0.8576 (tt0) cc_final: 0.8365 (tt0) REVERT: C 95 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6525 (mt-10) REVERT: C 101 ASP cc_start: 0.7997 (m-30) cc_final: 0.7610 (m-30) REVERT: C 123 GLN cc_start: 0.8304 (mt0) cc_final: 0.7731 (mt0) REVERT: C 124 ARG cc_start: 0.7071 (mtt-85) cc_final: 0.6808 (mtp85) REVERT: C 146 ASP cc_start: 0.7791 (m-30) cc_final: 0.7357 (m-30) REVERT: C 208 GLN cc_start: 0.7790 (mt0) cc_final: 0.7582 (mm110) REVERT: C 238 SER cc_start: 0.7568 (p) cc_final: 0.7096 (m) REVERT: C 248 ASN cc_start: 0.7326 (OUTLIER) cc_final: 0.6644 (m-40) REVERT: C 417 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6514 (mm-30) REVERT: C 445 ILE cc_start: 0.8008 (mt) cc_final: 0.7737 (mm) REVERT: C 560 LYS cc_start: 0.7588 (mmtt) cc_final: 0.7147 (mmmm) REVERT: C 591 LYS cc_start: 0.7643 (mtpt) cc_final: 0.7178 (mmpt) REVERT: C 594 ASP cc_start: 0.6675 (t0) cc_final: 0.6385 (t0) REVERT: C 602 ASN cc_start: 0.7461 (m110) cc_final: 0.7209 (m-40) REVERT: C 604 LYS cc_start: 0.7374 (mttp) cc_final: 0.7084 (mtpm) REVERT: C 631 LYS cc_start: 0.8456 (tttp) cc_final: 0.8218 (tttm) REVERT: C 657 MET cc_start: 0.6643 (mmm) cc_final: 0.6228 (mmm) REVERT: C 661 ASP cc_start: 0.7203 (m-30) cc_final: 0.5890 (t0) REVERT: C 747 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.7014 (mt) REVERT: C 768 ARG cc_start: 0.8389 (mtp85) cc_final: 0.7896 (ttt-90) REVERT: C 796 LYS cc_start: 0.6433 (mmtp) cc_final: 0.5962 (mmmm) REVERT: C 871 GLU cc_start: 0.7946 (tt0) cc_final: 0.7493 (tt0) REVERT: C 873 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7264 (mt-10) REVERT: C 962 LYS cc_start: 0.7533 (tttm) cc_final: 0.7303 (tttp) REVERT: C 987 ILE cc_start: 0.7917 (mt) cc_final: 0.7633 (mm) outliers start: 81 outliers final: 56 residues processed: 655 average time/residue: 2.0746 time to fit residues: 1673.1223 Evaluate side-chains 664 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 597 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 601 MET Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 747 ILE Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 923 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 990 THR Chi-restraints excluded: chain C residue 1004 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 30.0000 chunk 271 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 99 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 overall best weight: 7.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 241 GLN C 253 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 24744 Z= 0.418 Angle : 0.634 11.453 33594 Z= 0.338 Chirality : 0.050 1.464 3922 Planarity : 0.005 0.058 4281 Dihedral : 8.420 79.397 3628 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.82 % Allowed : 18.11 % Favored : 78.07 % 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: 0.65 (0.15), residues: 3136 helix: 1.36 (0.12), residues: 1678 sheet: 0.15 (0.24), residues: 439 loop : -0.94 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 635 HIS 0.007 0.001 HIS B 424 PHE 0.019 0.002 PHE C 682 TYR 0.017 0.002 TYR C 897 ARG 0.005 0.001 ARG C 872 *********************** 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 700 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 601 time to evaluate : 3.506 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 19 ILE cc_start: 0.7397 (mm) cc_final: 0.7190 (mt) REVERT: A 66 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 76 ARG cc_start: 0.7324 (mtm180) cc_final: 0.7027 (mtp85) REVERT: A 121 ASP cc_start: 0.7660 (m-30) cc_final: 0.7288 (m-30) REVERT: A 153 ASP cc_start: 0.7459 (m-30) cc_final: 0.7170 (m-30) REVERT: A 164 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: A 226 GLN cc_start: 0.6404 (mt0) cc_final: 0.6042 (mm-40) REVERT: A 247 LYS cc_start: 0.8010 (mttt) cc_final: 0.7550 (mttm) REVERT: A 315 LYS cc_start: 0.7523 (mttt) cc_final: 0.7184 (mttp) REVERT: A 355 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6909 (tpp) REVERT: A 400 LEU cc_start: 0.7376 (mt) cc_final: 0.7080 (mt) REVERT: A 608 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5996 (tt0) REVERT: A 696 LYS cc_start: 0.7076 (mmmm) cc_final: 0.6816 (mmmm) REVERT: A 818 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7451 (mm-30) REVERT: A 892 CYS cc_start: 0.7480 (m) cc_final: 0.6322 (t) REVERT: A 975 THR cc_start: 0.7844 (m) cc_final: 0.7563 (p) REVERT: B 3 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7367 (mp10) REVERT: B 8 ARG cc_start: 0.7456 (mtt90) cc_final: 0.7099 (mtt-85) REVERT: B 20 MET cc_start: 0.6561 (mtt) cc_final: 0.6043 (mmm) REVERT: B 21 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7530 (tt) REVERT: B 29 LYS cc_start: 0.7210 (mtpt) cc_final: 0.6864 (tptp) REVERT: B 42 THR cc_start: 0.8404 (p) cc_final: 0.7951 (m) REVERT: B 55 GLU cc_start: 0.7365 (tt0) cc_final: 0.6862 (tp30) REVERT: B 113 SER cc_start: 0.8633 (t) cc_final: 0.8339 (p) REVERT: B 148 ASN cc_start: 0.7845 (t0) cc_final: 0.7622 (t0) REVERT: B 174 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6411 (tt0) REVERT: B 208 GLN cc_start: 0.7259 (mt0) cc_final: 0.6790 (mm-40) REVERT: B 229 VAL cc_start: 0.8220 (p) cc_final: 0.7902 (t) REVERT: B 247 LYS cc_start: 0.6963 (mtpp) cc_final: 0.6418 (mttm) REVERT: B 280 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6098 (mtpp) REVERT: B 308 GLN cc_start: 0.6600 (tt0) cc_final: 0.6046 (tp-100) REVERT: B 309 ARG cc_start: 0.6893 (mmm160) cc_final: 0.6658 (mmm160) REVERT: B 325 LEU cc_start: 0.8206 (mt) cc_final: 0.7866 (mm) REVERT: B 335 LEU cc_start: 0.7066 (mt) cc_final: 0.6767 (mp) REVERT: B 346 GLU cc_start: 0.6414 (mt-10) cc_final: 0.6171 (tt0) REVERT: B 417 GLU cc_start: 0.7168 (tp30) cc_final: 0.6770 (mm-30) REVERT: B 429 THR cc_start: 0.8005 (m) cc_final: 0.7411 (p) REVERT: B 448 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8212 (t) REVERT: B 498 LYS cc_start: 0.7466 (tppt) cc_final: 0.7002 (mptm) REVERT: B 536 MET cc_start: 0.6717 (mmt) cc_final: 0.6149 (mmt) REVERT: B 579 GLN cc_start: 0.5847 (OUTLIER) cc_final: 0.5430 (tp-100) REVERT: B 637 LYS cc_start: 0.5795 (tppt) cc_final: 0.5515 (mtpp) REVERT: B 666 MET cc_start: 0.5744 (mmt) cc_final: 0.5286 (tpp) REVERT: B 718 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.7057 (ppt-90) REVERT: B 766 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7263 (mtp85) REVERT: B 782 MET cc_start: 0.7580 (mmp) cc_final: 0.7327 (mmp) REVERT: B 828 ILE cc_start: 0.8299 (mt) cc_final: 0.7941 (mp) REVERT: B 928 LYS cc_start: 0.7113 (mtmt) cc_final: 0.6808 (mtmm) REVERT: B 947 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7672 (mm) REVERT: B 967 LYS cc_start: 0.7007 (mmpt) cc_final: 0.6702 (mmmm) REVERT: B 977 HIS cc_start: 0.5971 (m-70) cc_final: 0.5641 (t-170) REVERT: B 980 LYS cc_start: 0.7724 (tttt) cc_final: 0.7167 (tmtm) REVERT: B 1027 PHE cc_start: 0.7194 (m-80) cc_final: 0.6949 (m-10) REVERT: C 20 MET cc_start: 0.8428 (mtp) cc_final: 0.8125 (mtp) REVERT: C 25 LEU cc_start: 0.8494 (mt) cc_final: 0.8217 (mt) REVERT: C 63 GLN cc_start: 0.7205 (mt0) cc_final: 0.6946 (mt0) REVERT: C 91 GLN cc_start: 0.8619 (tt0) cc_final: 0.8402 (tt0) REVERT: C 95 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6551 (mt-10) REVERT: C 101 ASP cc_start: 0.8000 (m-30) cc_final: 0.7604 (m-30) REVERT: C 124 ARG cc_start: 0.7063 (mtt-85) cc_final: 0.6803 (mtp85) REVERT: C 146 ASP cc_start: 0.7834 (m-30) cc_final: 0.7313 (m-30) REVERT: C 238 SER cc_start: 0.7554 (p) cc_final: 0.7116 (m) REVERT: C 241 GLN cc_start: 0.7584 (mt0) cc_final: 0.7279 (mt0) REVERT: C 253 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7535 (t0) REVERT: C 417 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6583 (mm-30) REVERT: C 445 ILE cc_start: 0.8173 (mt) cc_final: 0.7949 (mm) REVERT: C 560 LYS cc_start: 0.7649 (mmtt) cc_final: 0.7184 (mmmm) REVERT: C 591 LYS cc_start: 0.7792 (mtpt) cc_final: 0.7316 (mmtt) REVERT: C 602 ASN cc_start: 0.7493 (m110) cc_final: 0.7207 (m-40) REVERT: C 604 LYS cc_start: 0.7470 (mttp) cc_final: 0.7166 (mtpm) REVERT: C 631 LYS cc_start: 0.8499 (tttp) cc_final: 0.8286 (tttm) REVERT: C 657 MET cc_start: 0.6678 (mmm) cc_final: 0.6303 (mmm) REVERT: C 661 ASP cc_start: 0.7229 (m-30) cc_final: 0.5899 (t0) REVERT: C 747 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7045 (mt) REVERT: C 771 LYS cc_start: 0.8228 (mttp) cc_final: 0.7981 (mttm) REVERT: C 796 LYS cc_start: 0.6365 (mmtp) cc_final: 0.5874 (mmmm) REVERT: C 873 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7384 (mt-10) REVERT: C 962 LYS cc_start: 0.7491 (tttm) cc_final: 0.7096 (tttm) REVERT: C 984 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7510 (ttt180) REVERT: C 987 ILE cc_start: 0.8054 (mt) cc_final: 0.7788 (mm) outliers start: 99 outliers final: 71 residues processed: 659 average time/residue: 2.0794 time to fit residues: 1695.4195 Evaluate side-chains 672 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 589 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain B residue 766 ARG Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 601 MET Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 747 ILE Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 926 ILE Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 990 THR Chi-restraints excluded: chain C residue 1004 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.0770 chunk 34 optimal weight: 9.9990 chunk 171 optimal weight: 0.0570 chunk 220 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 overall best weight: 3.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24744 Z= 0.213 Angle : 0.553 11.384 33594 Z= 0.291 Chirality : 0.046 1.427 3922 Planarity : 0.005 0.054 4281 Dihedral : 8.118 77.827 3628 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.47 % Allowed : 18.92 % Favored : 77.61 % 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: 0.98 (0.15), residues: 3136 helix: 1.67 (0.13), residues: 1677 sheet: 0.18 (0.24), residues: 446 loop : -0.82 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 635 HIS 0.003 0.001 HIS B 500 PHE 0.018 0.001 PHE A 352 TYR 0.013 0.001 TYR C 35 ARG 0.006 0.000 ARG C 433 *********************** 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 685 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 595 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7380 (mm) cc_final: 0.7174 (mt) REVERT: A 66 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7963 (mt-10) REVERT: A 76 ARG cc_start: 0.7314 (mtm180) cc_final: 0.7028 (mtp85) REVERT: A 121 ASP cc_start: 0.7554 (m-30) cc_final: 0.7169 (m-30) REVERT: A 164 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: A 226 GLN cc_start: 0.6429 (mt0) cc_final: 0.6123 (mm-40) REVERT: A 247 LYS cc_start: 0.7975 (mttt) cc_final: 0.7527 (mttm) REVERT: A 315 LYS cc_start: 0.7512 (mttt) cc_final: 0.7176 (mttp) REVERT: A 328 ASP cc_start: 0.7132 (t0) cc_final: 0.6884 (t0) REVERT: A 355 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6842 (tpp) REVERT: A 400 LEU cc_start: 0.7329 (mt) cc_final: 0.7008 (mt) REVERT: A 608 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.6029 (tt0) REVERT: A 684 LEU cc_start: 0.7011 (tp) cc_final: 0.6710 (tm) REVERT: A 696 LYS cc_start: 0.6984 (mmmm) cc_final: 0.6734 (mmmm) REVERT: A 818 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7352 (mm-30) REVERT: A 890 PHE cc_start: 0.7564 (t80) cc_final: 0.7093 (t80) REVERT: A 892 CYS cc_start: 0.7268 (m) cc_final: 0.6122 (t) REVERT: A 975 THR cc_start: 0.7799 (m) cc_final: 0.7518 (p) REVERT: B 3 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7395 (mp10) REVERT: B 8 ARG cc_start: 0.7435 (mtt90) cc_final: 0.7126 (mtt-85) REVERT: B 20 MET cc_start: 0.6532 (mtt) cc_final: 0.6008 (mmm) REVERT: B 21 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7533 (tt) REVERT: B 42 THR cc_start: 0.8410 (p) cc_final: 0.7979 (m) REVERT: B 55 GLU cc_start: 0.7370 (tt0) cc_final: 0.6884 (tp30) REVERT: B 113 SER cc_start: 0.8559 (t) cc_final: 0.8287 (p) REVERT: B 148 ASN cc_start: 0.7860 (t0) cc_final: 0.7657 (t0) REVERT: B 174 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6367 (tt0) REVERT: B 208 GLN cc_start: 0.7335 (mt0) cc_final: 0.6800 (mm-40) REVERT: B 229 VAL cc_start: 0.8204 (p) cc_final: 0.7876 (t) REVERT: B 247 LYS cc_start: 0.6946 (mtpp) cc_final: 0.6392 (mttm) REVERT: B 280 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6083 (mtpp) REVERT: B 289 LEU cc_start: 0.7852 (tt) cc_final: 0.7609 (tp) REVERT: B 308 GLN cc_start: 0.6589 (tt0) cc_final: 0.6037 (tp-100) REVERT: B 325 LEU cc_start: 0.8190 (mt) cc_final: 0.7863 (mm) REVERT: B 335 LEU cc_start: 0.7022 (mt) cc_final: 0.6743 (mp) REVERT: B 346 GLU cc_start: 0.6436 (mt-10) cc_final: 0.6169 (tt0) REVERT: B 417 GLU cc_start: 0.7212 (tp30) cc_final: 0.6829 (mm-30) REVERT: B 429 THR cc_start: 0.8079 (m) cc_final: 0.7530 (p) REVERT: B 448 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8195 (t) REVERT: B 498 LYS cc_start: 0.7417 (tppt) cc_final: 0.6899 (mptm) REVERT: B 536 MET cc_start: 0.6684 (mmt) cc_final: 0.6268 (mmt) REVERT: B 553 LEU cc_start: 0.7795 (tp) cc_final: 0.7439 (tm) REVERT: B 579 GLN cc_start: 0.5881 (OUTLIER) cc_final: 0.5502 (tp-100) REVERT: B 637 LYS cc_start: 0.5819 (tppt) cc_final: 0.5535 (mtpp) REVERT: B 666 MET cc_start: 0.5686 (mmt) cc_final: 0.5225 (tpp) REVERT: B 718 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.7048 (ppt-90) REVERT: B 766 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6850 (mtp85) REVERT: B 782 MET cc_start: 0.7528 (mmp) cc_final: 0.7205 (mmp) REVERT: B 807 THR cc_start: 0.7061 (OUTLIER) cc_final: 0.6663 (t) REVERT: B 928 LYS cc_start: 0.7339 (mtmt) cc_final: 0.7041 (mtmm) REVERT: B 947 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7679 (mm) REVERT: B 949 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7467 (tt) REVERT: B 967 LYS cc_start: 0.6996 (mmpt) cc_final: 0.6695 (mmmm) REVERT: B 977 HIS cc_start: 0.5954 (m-70) cc_final: 0.5671 (t-170) REVERT: B 980 LYS cc_start: 0.7657 (tttt) cc_final: 0.7104 (tmtm) REVERT: C 20 MET cc_start: 0.8372 (mtp) cc_final: 0.8140 (mtp) REVERT: C 25 LEU cc_start: 0.8484 (mt) cc_final: 0.8224 (mt) REVERT: C 63 GLN cc_start: 0.7181 (mt0) cc_final: 0.6850 (mt0) REVERT: C 95 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6514 (mt-10) REVERT: C 101 ASP cc_start: 0.7975 (m-30) cc_final: 0.7602 (m-30) REVERT: C 121 ASP cc_start: 0.6529 (m-30) cc_final: 0.6262 (m-30) REVERT: C 123 GLN cc_start: 0.8252 (mt0) cc_final: 0.7679 (mt0) REVERT: C 124 ARG cc_start: 0.7077 (mtt-85) cc_final: 0.6808 (mtp85) REVERT: C 146 ASP cc_start: 0.7796 (m-30) cc_final: 0.7362 (m-30) REVERT: C 238 SER cc_start: 0.7544 (p) cc_final: 0.7076 (m) REVERT: C 248 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.6675 (m-40) REVERT: C 417 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6503 (mm-30) REVERT: C 445 ILE cc_start: 0.8032 (mt) cc_final: 0.7798 (mm) REVERT: C 560 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7152 (mmmm) REVERT: C 591 LYS cc_start: 0.7680 (mtpt) cc_final: 0.7253 (mmtt) REVERT: C 594 ASP cc_start: 0.6735 (t0) cc_final: 0.6320 (t0) REVERT: C 602 ASN cc_start: 0.7456 (m110) cc_final: 0.7184 (m-40) REVERT: C 604 LYS cc_start: 0.7400 (mttp) cc_final: 0.7106 (mtpm) REVERT: C 631 LYS cc_start: 0.8441 (tttp) cc_final: 0.8195 (tttm) REVERT: C 657 MET cc_start: 0.6693 (mmm) cc_final: 0.6289 (mmm) REVERT: C 661 ASP cc_start: 0.7210 (m-30) cc_final: 0.5870 (t0) REVERT: C 684 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8318 (tp) REVERT: C 747 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7019 (mt) REVERT: C 796 LYS cc_start: 0.6336 (mmtp) cc_final: 0.5837 (mmmm) REVERT: C 871 GLU cc_start: 0.7943 (tt0) cc_final: 0.7564 (tt0) REVERT: C 873 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7234 (mt-10) REVERT: C 962 LYS cc_start: 0.7529 (tttm) cc_final: 0.7138 (tttm) REVERT: C 987 ILE cc_start: 0.7921 (mt) cc_final: 0.7635 (mm) outliers start: 90 outliers final: 67 residues processed: 650 average time/residue: 2.0401 time to fit residues: 1647.5745 Evaluate side-chains 677 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 595 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain B residue 766 ARG Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 601 MET Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 747 ILE Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 923 LEU Chi-restraints excluded: chain C residue 926 ILE Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 990 THR Chi-restraints excluded: chain C residue 1004 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 204 optimal weight: 0.5980 chunk 148 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 ASN ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 241 GLN C 877 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24744 Z= 0.171 Angle : 0.524 11.306 33594 Z= 0.272 Chirality : 0.046 1.404 3922 Planarity : 0.004 0.055 4281 Dihedral : 7.752 76.578 3627 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.01 % Allowed : 19.65 % Favored : 77.34 % 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: 1.96 (0.13), residues: 1672 sheet: 0.25 (0.24), residues: 450 loop : -0.68 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 635 HIS 0.011 0.001 HIS C 977 PHE 0.010 0.001 PHE C 682 TYR 0.012 0.001 TYR C 35 ARG 0.007 0.000 ARG C 433 *********************** 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 687 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 609 time to evaluate : 4.194 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 66 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7813 (tt0) REVERT: A 76 ARG cc_start: 0.7290 (mtm180) cc_final: 0.7020 (mtp85) REVERT: A 121 ASP cc_start: 0.7484 (m-30) cc_final: 0.7140 (m-30) REVERT: A 153 ASP cc_start: 0.7342 (m-30) cc_final: 0.7075 (m-30) REVERT: A 226 GLN cc_start: 0.6417 (mt0) cc_final: 0.6130 (mm-40) REVERT: A 247 LYS cc_start: 0.8003 (mttt) cc_final: 0.7548 (mttm) REVERT: A 315 LYS cc_start: 0.7571 (mttt) cc_final: 0.7233 (mttp) REVERT: A 328 ASP cc_start: 0.7054 (t0) cc_final: 0.6805 (t0) REVERT: A 355 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6836 (tpp) REVERT: A 400 LEU cc_start: 0.7192 (mt) cc_final: 0.6851 (mt) REVERT: A 684 LEU cc_start: 0.6973 (tp) cc_final: 0.6745 (tm) REVERT: A 696 LYS cc_start: 0.6965 (mmmm) cc_final: 0.6705 (mmmm) REVERT: A 818 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7344 (mm-30) REVERT: A 890 PHE cc_start: 0.7536 (t80) cc_final: 0.7151 (t80) REVERT: A 892 CYS cc_start: 0.7246 (m) cc_final: 0.6104 (t) REVERT: A 975 THR cc_start: 0.7794 (m) cc_final: 0.7517 (p) REVERT: B 3 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7412 (mp10) REVERT: B 8 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7150 (mtt-85) REVERT: B 20 MET cc_start: 0.6521 (mtt) cc_final: 0.5997 (mmm) REVERT: B 21 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7544 (tt) REVERT: B 42 THR cc_start: 0.8381 (p) cc_final: 0.7957 (m) REVERT: B 55 GLU cc_start: 0.7375 (tt0) cc_final: 0.6883 (tp30) REVERT: B 113 SER cc_start: 0.8560 (t) cc_final: 0.8257 (p) REVERT: B 174 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6388 (tt0) REVERT: B 208 GLN cc_start: 0.7359 (mt0) cc_final: 0.6829 (mm-40) REVERT: B 229 VAL cc_start: 0.8189 (p) cc_final: 0.7858 (t) REVERT: B 247 LYS cc_start: 0.6875 (mtpp) cc_final: 0.6216 (mttm) REVERT: B 289 LEU cc_start: 0.7830 (tt) cc_final: 0.7537 (tp) REVERT: B 308 GLN cc_start: 0.6570 (tt0) cc_final: 0.6024 (tp-100) REVERT: B 335 LEU cc_start: 0.6897 (mt) cc_final: 0.6637 (mp) REVERT: B 346 GLU cc_start: 0.6333 (mt-10) cc_final: 0.6073 (tt0) REVERT: B 417 GLU cc_start: 0.7169 (tp30) cc_final: 0.6770 (mm-30) REVERT: B 429 THR cc_start: 0.8076 (m) cc_final: 0.7642 (p) REVERT: B 498 LYS cc_start: 0.7341 (tppt) cc_final: 0.6845 (mptm) REVERT: B 525 MET cc_start: 0.6182 (tpp) cc_final: 0.5845 (tpt) REVERT: B 536 MET cc_start: 0.6655 (mmt) cc_final: 0.6239 (mmt) REVERT: B 553 LEU cc_start: 0.7774 (tp) cc_final: 0.7442 (tm) REVERT: B 579 GLN cc_start: 0.5778 (OUTLIER) cc_final: 0.5474 (tp-100) REVERT: B 637 LYS cc_start: 0.5897 (tppt) cc_final: 0.5523 (mtpm) REVERT: B 666 MET cc_start: 0.5709 (mmt) cc_final: 0.5254 (tpp) REVERT: B 718 ARG cc_start: 0.7232 (ptt90) cc_final: 0.7003 (ppt-90) REVERT: B 782 MET cc_start: 0.7530 (mmp) cc_final: 0.7212 (mmp) REVERT: B 788 ASN cc_start: 0.7697 (m-40) cc_final: 0.7438 (m-40) REVERT: B 807 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6724 (t) REVERT: B 928 LYS cc_start: 0.7341 (mtmt) cc_final: 0.7044 (mtmm) REVERT: B 947 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7598 (mm) REVERT: B 949 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7441 (tt) REVERT: B 967 LYS cc_start: 0.7017 (mmpt) cc_final: 0.6705 (mmmm) REVERT: B 977 HIS cc_start: 0.5939 (m-70) cc_final: 0.5692 (t-170) REVERT: B 980 LYS cc_start: 0.7630 (tttt) cc_final: 0.7065 (tmtm) REVERT: C 25 LEU cc_start: 0.8425 (mt) cc_final: 0.8172 (mt) REVERT: C 63 GLN cc_start: 0.7123 (mt0) cc_final: 0.6828 (mt0) REVERT: C 89 SER cc_start: 0.8726 (t) cc_final: 0.8399 (m) REVERT: C 91 GLN cc_start: 0.8577 (tt0) cc_final: 0.8376 (tt0) REVERT: C 95 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6447 (mt-10) REVERT: C 121 ASP cc_start: 0.6601 (m-30) cc_final: 0.6262 (m-30) REVERT: C 123 GLN cc_start: 0.8271 (mt0) cc_final: 0.7644 (mt0) REVERT: C 124 ARG cc_start: 0.7098 (mtt-85) cc_final: 0.6825 (mtp85) REVERT: C 146 ASP cc_start: 0.7789 (m-30) cc_final: 0.7363 (m-30) REVERT: C 241 GLN cc_start: 0.7591 (mt0) cc_final: 0.7342 (mt0) REVERT: C 417 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6502 (mm-30) REVERT: C 560 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7115 (mmmm) REVERT: C 591 LYS cc_start: 0.7556 (mtpt) cc_final: 0.7068 (mmpt) REVERT: C 594 ASP cc_start: 0.6732 (t0) cc_final: 0.6363 (t0) REVERT: C 602 ASN cc_start: 0.7376 (m110) cc_final: 0.7156 (m-40) REVERT: C 604 LYS cc_start: 0.7292 (mttp) cc_final: 0.7013 (mtpm) REVERT: C 631 LYS cc_start: 0.8409 (tttp) cc_final: 0.8184 (tttm) REVERT: C 657 MET cc_start: 0.6632 (mmm) cc_final: 0.6231 (mmm) REVERT: C 661 ASP cc_start: 0.7229 (m-30) cc_final: 0.5881 (t0) REVERT: C 684 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8336 (tp) REVERT: C 747 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7041 (mt) REVERT: C 796 LYS cc_start: 0.6323 (mmtp) cc_final: 0.5817 (mmmm) REVERT: C 871 GLU cc_start: 0.7968 (tt0) cc_final: 0.7660 (tt0) REVERT: C 873 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7240 (mt-10) REVERT: C 955 ILE cc_start: 0.8394 (mm) cc_final: 0.8161 (mp) REVERT: C 987 ILE cc_start: 0.7906 (mt) cc_final: 0.7642 (mm) REVERT: C 997 VAL cc_start: 0.8602 (m) cc_final: 0.8133 (p) outliers start: 78 outliers final: 53 residues processed: 653 average time/residue: 2.1063 time to fit residues: 1720.1253 Evaluate side-chains 655 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 594 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 601 MET Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 747 ILE Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 923 LEU Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 990 THR Chi-restraints excluded: chain C residue 1004 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 9.9990 chunk 288 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 280 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 253 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 279 optimal weight: 0.9980 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 722 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 977 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24744 Z= 0.267 Angle : 0.560 11.388 33594 Z= 0.293 Chirality : 0.047 1.435 3922 Planarity : 0.005 0.055 4281 Dihedral : 7.842 76.444 3627 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.82 % Allowed : 20.15 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3136 helix: 1.81 (0.13), residues: 1675 sheet: 0.17 (0.24), residues: 453 loop : -0.73 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 635 HIS 0.007 0.001 HIS C 977 PHE 0.020 0.001 PHE A 352 TYR 0.017 0.002 TYR C 35 ARG 0.007 0.000 ARG C 433 *********************** 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 670 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 597 time to evaluate : 3.356 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 66 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7943 (mt-10) REVERT: A 76 ARG cc_start: 0.7313 (mtm180) cc_final: 0.7055 (mtp85) REVERT: A 95 GLU cc_start: 0.6073 (mm-30) cc_final: 0.5777 (mm-30) REVERT: A 121 ASP cc_start: 0.7570 (m-30) cc_final: 0.7183 (m-30) REVERT: A 153 ASP cc_start: 0.7430 (m-30) cc_final: 0.7161 (m-30) REVERT: A 164 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: A 226 GLN cc_start: 0.6455 (mt0) cc_final: 0.6142 (mm-40) REVERT: A 247 LYS cc_start: 0.7969 (mttt) cc_final: 0.7515 (mttm) REVERT: A 315 LYS cc_start: 0.7582 (mttt) cc_final: 0.7248 (mttp) REVERT: A 328 ASP cc_start: 0.7112 (t0) cc_final: 0.6865 (t0) REVERT: A 355 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: A 400 LEU cc_start: 0.7310 (mt) cc_final: 0.6992 (mt) REVERT: A 684 LEU cc_start: 0.7008 (tp) cc_final: 0.6738 (tm) REVERT: A 696 LYS cc_start: 0.6971 (mmmm) cc_final: 0.6720 (mmmm) REVERT: A 818 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7344 (mm-30) REVERT: A 890 PHE cc_start: 0.7559 (t80) cc_final: 0.7094 (t80) REVERT: A 892 CYS cc_start: 0.7376 (m) cc_final: 0.6258 (t) REVERT: A 975 THR cc_start: 0.7745 (m) cc_final: 0.7477 (p) REVERT: B 3 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7411 (mp10) REVERT: B 8 ARG cc_start: 0.7495 (mtt90) cc_final: 0.7147 (mtt-85) REVERT: B 20 MET cc_start: 0.6550 (mtt) cc_final: 0.6042 (mmm) REVERT: B 21 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7560 (tt) REVERT: B 42 THR cc_start: 0.8384 (p) cc_final: 0.7953 (m) REVERT: B 55 GLU cc_start: 0.7357 (tt0) cc_final: 0.6863 (tp30) REVERT: B 113 SER cc_start: 0.8570 (t) cc_final: 0.8252 (p) REVERT: B 174 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6402 (tt0) REVERT: B 208 GLN cc_start: 0.7365 (mt0) cc_final: 0.6838 (mm-40) REVERT: B 229 VAL cc_start: 0.8196 (p) cc_final: 0.7862 (t) REVERT: B 247 LYS cc_start: 0.6857 (mtpp) cc_final: 0.6261 (mttm) REVERT: B 308 GLN cc_start: 0.6590 (tt0) cc_final: 0.6031 (tp-100) REVERT: B 335 LEU cc_start: 0.6978 (mt) cc_final: 0.6711 (mp) REVERT: B 346 GLU cc_start: 0.6407 (mt-10) cc_final: 0.6127 (tt0) REVERT: B 417 GLU cc_start: 0.7230 (tp30) cc_final: 0.6838 (mm-30) REVERT: B 429 THR cc_start: 0.8083 (m) cc_final: 0.7655 (p) REVERT: B 498 LYS cc_start: 0.7367 (tppt) cc_final: 0.6889 (mptm) REVERT: B 536 MET cc_start: 0.6664 (mmt) cc_final: 0.6112 (mmt) REVERT: B 553 LEU cc_start: 0.7810 (tp) cc_final: 0.7478 (tm) REVERT: B 579 GLN cc_start: 0.5762 (OUTLIER) cc_final: 0.5321 (tp-100) REVERT: B 637 LYS cc_start: 0.5830 (tppt) cc_final: 0.5538 (mtpp) REVERT: B 666 MET cc_start: 0.5702 (mmt) cc_final: 0.5244 (tpp) REVERT: B 718 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.7011 (ppt-90) REVERT: B 782 MET cc_start: 0.7534 (mmp) cc_final: 0.7291 (mmp) REVERT: B 807 THR cc_start: 0.7091 (OUTLIER) cc_final: 0.6721 (t) REVERT: B 928 LYS cc_start: 0.7305 (mtmt) cc_final: 0.7006 (mtmm) REVERT: B 947 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7599 (mm) REVERT: B 967 LYS cc_start: 0.7067 (mmpt) cc_final: 0.6750 (mmmm) REVERT: B 977 HIS cc_start: 0.5966 (m-70) cc_final: 0.5672 (t-170) REVERT: B 980 LYS cc_start: 0.7707 (tttt) cc_final: 0.7129 (tmtm) REVERT: C 25 LEU cc_start: 0.8446 (mt) cc_final: 0.8177 (mt) REVERT: C 63 GLN cc_start: 0.7116 (mt0) cc_final: 0.6868 (mt0) REVERT: C 89 SER cc_start: 0.8715 (t) cc_final: 0.8390 (m) REVERT: C 95 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6528 (mt-10) REVERT: C 101 ASP cc_start: 0.7962 (m-30) cc_final: 0.7589 (m-30) REVERT: C 121 ASP cc_start: 0.6604 (m-30) cc_final: 0.6274 (m-30) REVERT: C 124 ARG cc_start: 0.7098 (mtt-85) cc_final: 0.6826 (mtp85) REVERT: C 146 ASP cc_start: 0.7795 (m-30) cc_final: 0.7360 (m-30) REVERT: C 417 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6500 (mm-30) REVERT: C 560 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7175 (mmmm) REVERT: C 591 LYS cc_start: 0.7681 (mtpt) cc_final: 0.7223 (mmpt) REVERT: C 594 ASP cc_start: 0.6712 (t0) cc_final: 0.6358 (t0) REVERT: C 602 ASN cc_start: 0.7389 (m110) cc_final: 0.7138 (m-40) REVERT: C 604 LYS cc_start: 0.7334 (mttp) cc_final: 0.7028 (mtpm) REVERT: C 631 LYS cc_start: 0.8438 (tttp) cc_final: 0.8224 (tttm) REVERT: C 657 MET cc_start: 0.6646 (mmm) cc_final: 0.6243 (mmm) REVERT: C 661 ASP cc_start: 0.7248 (m-30) cc_final: 0.5877 (t0) REVERT: C 684 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8338 (tp) REVERT: C 747 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7045 (mt) REVERT: C 796 LYS cc_start: 0.6316 (mmtp) cc_final: 0.5827 (mmmm) REVERT: C 871 GLU cc_start: 0.7961 (tt0) cc_final: 0.7697 (tt0) REVERT: C 873 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7263 (mt-10) REVERT: C 984 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7482 (ttt180) REVERT: C 987 ILE cc_start: 0.7990 (mt) cc_final: 0.7755 (mm) outliers start: 73 outliers final: 58 residues processed: 641 average time/residue: 2.0436 time to fit residues: 1620.8199 Evaluate side-chains 663 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 596 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 601 MET Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 747 ILE Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 990 THR Chi-restraints excluded: chain C residue 1004 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 310 optimal weight: 10.0000 chunk 286 optimal weight: 0.7980 chunk 247 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 191 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 241 GLN C 722 GLN C 877 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24744 Z= 0.219 Angle : 0.547 11.362 33594 Z= 0.284 Chirality : 0.046 1.420 3922 Planarity : 0.004 0.059 4281 Dihedral : 7.737 76.426 3627 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.66 % Allowed : 20.35 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3136 helix: 1.87 (0.13), residues: 1673 sheet: 0.17 (0.24), residues: 453 loop : -0.69 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 635 HIS 0.011 0.001 HIS C 977 PHE 0.012 0.001 PHE C 682 TYR 0.018 0.001 TYR C 35 ARG 0.007 0.000 ARG C 433 ********************** 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 667 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 598 time to evaluate : 3.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7832 (tt0) REVERT: A 76 ARG cc_start: 0.7293 (mtm180) cc_final: 0.7021 (mtp85) REVERT: A 121 ASP cc_start: 0.7497 (m-30) cc_final: 0.7144 (m-30) REVERT: A 153 ASP cc_start: 0.7409 (m-30) cc_final: 0.7138 (m-30) REVERT: A 164 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: A 226 GLN cc_start: 0.6448 (mt0) cc_final: 0.6148 (mm-40) REVERT: A 247 LYS cc_start: 0.8011 (mttt) cc_final: 0.7563 (mttm) REVERT: A 315 LYS cc_start: 0.7564 (mttt) cc_final: 0.7235 (mttp) REVERT: A 328 ASP cc_start: 0.7088 (t0) cc_final: 0.6851 (t0) REVERT: A 355 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6844 (tpp) REVERT: A 400 LEU cc_start: 0.7289 (mt) cc_final: 0.6946 (mt) REVERT: A 684 LEU cc_start: 0.6994 (tp) cc_final: 0.6736 (tm) REVERT: A 696 LYS cc_start: 0.6964 (mmmm) cc_final: 0.6710 (mmmm) REVERT: A 818 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7346 (mm-30) REVERT: A 890 PHE cc_start: 0.7537 (t80) cc_final: 0.7154 (t80) REVERT: A 892 CYS cc_start: 0.7364 (m) cc_final: 0.6251 (t) REVERT: A 975 THR cc_start: 0.7747 (m) cc_final: 0.7484 (p) REVERT: B 3 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7405 (mp10) REVERT: B 8 ARG cc_start: 0.7479 (mtt90) cc_final: 0.7138 (mtt-85) REVERT: B 20 MET cc_start: 0.6548 (mtt) cc_final: 0.6047 (mmm) REVERT: B 21 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7546 (tt) REVERT: B 42 THR cc_start: 0.8384 (p) cc_final: 0.7961 (m) REVERT: B 55 GLU cc_start: 0.7383 (tt0) cc_final: 0.6887 (tp30) REVERT: B 113 SER cc_start: 0.8599 (t) cc_final: 0.8301 (p) REVERT: B 174 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6342 (tt0) REVERT: B 208 GLN cc_start: 0.7351 (mt0) cc_final: 0.6828 (mm-40) REVERT: B 229 VAL cc_start: 0.8186 (p) cc_final: 0.7849 (t) REVERT: B 247 LYS cc_start: 0.6844 (mtpp) cc_final: 0.6203 (mttm) REVERT: B 308 GLN cc_start: 0.6591 (tt0) cc_final: 0.6035 (tp-100) REVERT: B 335 LEU cc_start: 0.6908 (mt) cc_final: 0.6646 (mp) REVERT: B 346 GLU cc_start: 0.6389 (mt-10) cc_final: 0.6100 (tt0) REVERT: B 417 GLU cc_start: 0.7177 (tp30) cc_final: 0.6797 (mm-30) REVERT: B 429 THR cc_start: 0.8093 (m) cc_final: 0.7667 (p) REVERT: B 498 LYS cc_start: 0.7350 (tppt) cc_final: 0.6860 (mptm) REVERT: B 536 MET cc_start: 0.6654 (mmt) cc_final: 0.6101 (mmt) REVERT: B 553 LEU cc_start: 0.7802 (tp) cc_final: 0.7469 (tm) REVERT: B 579 GLN cc_start: 0.5768 (OUTLIER) cc_final: 0.5342 (tp-100) REVERT: B 637 LYS cc_start: 0.5841 (tppt) cc_final: 0.5616 (mtpp) REVERT: B 666 MET cc_start: 0.5700 (mmt) cc_final: 0.5240 (tpp) REVERT: B 718 ARG cc_start: 0.7226 (ptt90) cc_final: 0.6995 (ppt-90) REVERT: B 782 MET cc_start: 0.7529 (mmp) cc_final: 0.7200 (mmp) REVERT: B 807 THR cc_start: 0.7083 (OUTLIER) cc_final: 0.6751 (t) REVERT: B 928 LYS cc_start: 0.7338 (mtmt) cc_final: 0.7053 (mtmm) REVERT: B 947 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7602 (mm) REVERT: B 967 LYS cc_start: 0.7120 (mmpt) cc_final: 0.6822 (mmtm) REVERT: B 977 HIS cc_start: 0.5928 (m-70) cc_final: 0.5676 (t-170) REVERT: B 980 LYS cc_start: 0.7638 (tttt) cc_final: 0.7079 (tmtm) REVERT: C 25 LEU cc_start: 0.8431 (mt) cc_final: 0.8162 (mt) REVERT: C 63 GLN cc_start: 0.7120 (mt0) cc_final: 0.6829 (mt0) REVERT: C 89 SER cc_start: 0.8714 (t) cc_final: 0.8389 (m) REVERT: C 95 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6547 (mt-10) REVERT: C 121 ASP cc_start: 0.6575 (m-30) cc_final: 0.6227 (m-30) REVERT: C 124 ARG cc_start: 0.7105 (mtt-85) cc_final: 0.6833 (mtp85) REVERT: C 146 ASP cc_start: 0.7790 (m-30) cc_final: 0.7354 (m-30) REVERT: C 241 GLN cc_start: 0.7570 (mt0) cc_final: 0.7317 (mt0) REVERT: C 417 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6426 (mm-30) REVERT: C 560 LYS cc_start: 0.7624 (mmtt) cc_final: 0.7178 (mmmm) REVERT: C 591 LYS cc_start: 0.7621 (mtpt) cc_final: 0.7144 (mmpt) REVERT: C 594 ASP cc_start: 0.6737 (t0) cc_final: 0.6380 (t0) REVERT: C 602 ASN cc_start: 0.7386 (m110) cc_final: 0.7142 (m-40) REVERT: C 604 LYS cc_start: 0.7244 (mttp) cc_final: 0.6962 (mtpm) REVERT: C 631 LYS cc_start: 0.8425 (tttp) cc_final: 0.8192 (tttm) REVERT: C 642 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6703 (mp0) REVERT: C 657 MET cc_start: 0.6639 (mmm) cc_final: 0.6242 (mmm) REVERT: C 661 ASP cc_start: 0.7248 (m-30) cc_final: 0.5870 (t0) REVERT: C 684 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8323 (tp) REVERT: C 747 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7033 (mt) REVERT: C 796 LYS cc_start: 0.6299 (mmtp) cc_final: 0.5807 (mmmm) REVERT: C 871 GLU cc_start: 0.7939 (tt0) cc_final: 0.7699 (tt0) REVERT: C 873 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7208 (mt-10) REVERT: C 984 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7477 (ttt180) REVERT: C 987 ILE cc_start: 0.7935 (mt) cc_final: 0.7701 (mm) outliers start: 69 outliers final: 57 residues processed: 641 average time/residue: 2.0920 time to fit residues: 1662.7249 Evaluate side-chains 660 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 595 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 601 MET Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 747 ILE Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 990 THR Chi-restraints excluded: chain C residue 1004 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.1980 chunk 263 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 736 GLN C 104 GLN C 276 GLN C 530 GLN C 722 GLN C 877 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.154580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.129335 restraints weight = 70145.826| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 0.93 r_work: 0.3132 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24744 Z= 0.259 Angle : 0.565 11.409 33594 Z= 0.295 Chirality : 0.047 1.435 3922 Planarity : 0.005 0.059 4281 Dihedral : 7.734 76.388 3626 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.05 % Allowed : 20.08 % Favored : 76.87 % 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: 1.10 (0.15), residues: 3136 helix: 1.77 (0.13), residues: 1677 sheet: 0.18 (0.24), residues: 448 loop : -0.75 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 635 HIS 0.007 0.001 HIS C 977 PHE 0.022 0.001 PHE A 352 TYR 0.021 0.002 TYR C 35 ARG 0.008 0.000 ARG C 433 =============================================================================== Job complete usr+sys time: 21946.95 seconds wall clock time: 386 minutes 44.24 seconds (23204.24 seconds total)