Starting phenix.real_space_refine on Mon Jul 6 04:41:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dds_27340/07_2026/8dds_27340.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dds_27340/07_2026/8dds_27340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dds_27340/07_2026/8dds_27340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dds_27340/07_2026/8dds_27340.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dds_27340/07_2026/8dds_27340.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dds_27340/07_2026/8dds_27340.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dds_27340/07_2026/8dds_27340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dds_27340/07_2026/8dds_27340.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 232 5.16 5 Na 2 4.78 5 C 20916 2.51 5 N 5376 2.21 5 O 5688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32230 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 132 Unusual residues: {' NA': 1, '3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 132 Unusual residues: {' NA': 1, '3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N APHE A 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE A 913 " occ=0.47 residue: pdb=" N AMET A1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET A1011 " occ=0.57 residue: pdb=" N APHE B 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE B 913 " occ=0.47 residue: pdb=" N AMET B1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET B1011 " occ=0.57 residue: pdb=" N APHE C 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE C 913 " occ=0.47 residue: pdb=" N AMET C1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET C1011 " occ=0.57 residue: pdb=" N APHE D 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE D 913 " occ=0.47 residue: pdb=" N AMET D1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET D1011 " occ=0.57 Time building chain proxies: 7.40, per 1000 atoms: 0.23 Number of scatterers: 32230 At special positions: 0 Unit cell: (143.64, 143.64, 159.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 232 16.00 P 16 15.00 Na 2 11.00 O 5688 8.00 N 5376 7.00 C 20916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7432 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 12 sheets defined 65.1% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 165 through 175 Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.843A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.647A pdb=" N HIS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.218A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.830A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.982A pdb=" N LYS A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.668A pdb=" N THR A 402 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.568A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 466 Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.501A pdb=" N GLN A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 528 removed outlier: 3.640A pdb=" N ASN A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 545 removed outlier: 3.662A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.701A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.032A pdb=" N ASN A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 648 removed outlier: 4.339A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.881A pdb=" N GLN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 685 Processing helix chain 'A' and resid 690 through 717 Processing helix chain 'A' and resid 717 through 725 Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 752 through 765 removed outlier: 3.700A pdb=" N GLY A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 862 through 866 removed outlier: 3.870A pdb=" N GLU A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 862 through 866' Processing helix chain 'A' and resid 867 through 869 No H-bonds generated for 'chain 'A' and resid 867 through 869' Processing helix chain 'A' and resid 870 through 893 removed outlier: 3.622A pdb=" N TYR A 891 " --> pdb=" O MET A 887 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 892 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 925 Processing helix chain 'A' and resid 930 through 940 removed outlier: 4.043A pdb=" N LYS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 962 removed outlier: 3.704A pdb=" N VAL A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 Processing helix chain 'A' and resid 985 through 991 removed outlier: 4.159A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1033 removed outlier: 3.782A pdb=" N LYS A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1046 removed outlier: 3.504A pdb=" N ASN A1045 " --> pdb=" O LYS A1041 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1041 through 1046' Processing helix chain 'A' and resid 1047 through 1054 removed outlier: 3.904A pdb=" N ILE A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1104 removed outlier: 3.521A pdb=" N MET A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A1097 " --> pdb=" O ALA A1093 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A1100 " --> pdb=" O ALA A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1118 through 1143 removed outlier: 4.577A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A1143 " --> pdb=" O THR A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1150 Processing helix chain 'A' and resid 1151 through 1164 removed outlier: 3.605A pdb=" N ILE A1159 " --> pdb=" O HIS A1155 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS A1164 " --> pdb=" O PHE A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1214 Processing helix chain 'A' and resid 1215 through 1240 removed outlier: 3.586A pdb=" N THR A1223 " --> pdb=" O ARG A1219 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 228 through 239 removed outlier: 3.560A pdb=" N HIS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 279 through 283 removed outlier: 4.032A pdb=" N LYS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 343 through 354 removed outlier: 4.379A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.972A pdb=" N LYS B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 439 through 453 removed outlier: 3.553A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 466 Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 528 removed outlier: 3.638A pdb=" N ASN B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.715A pdb=" N LEU B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 545 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.715A pdb=" N GLY B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.983A pdb=" N ASN B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 648 removed outlier: 4.337A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.846A pdb=" N GLN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 685 Processing helix chain 'B' and resid 690 through 717 Processing helix chain 'B' and resid 717 through 725 Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 746 through 751 Processing helix chain 'B' and resid 752 through 764 Processing helix chain 'B' and resid 774 through 782 Processing helix chain 'B' and resid 783 through 787 Processing helix chain 'B' and resid 862 through 866 removed outlier: 3.868A pdb=" N GLU B 866 " --> pdb=" O ARG B 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 862 through 866' Processing helix chain 'B' and resid 867 through 869 No H-bonds generated for 'chain 'B' and resid 867 through 869' Processing helix chain 'B' and resid 870 through 893 removed outlier: 3.631A pdb=" N TYR B 891 " --> pdb=" O MET B 887 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 892 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 893 " --> pdb=" O PHE B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 925 Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 941 through 944 removed outlier: 3.674A pdb=" N ASN B 944 " --> pdb=" O GLU B 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 945 through 962 removed outlier: 3.509A pdb=" N LEU B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 985 removed outlier: 4.643A pdb=" N ILE B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 991 removed outlier: 3.798A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1033 removed outlier: 3.930A pdb=" N ILE B1008 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1046 removed outlier: 3.689A pdb=" N ILE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1054 removed outlier: 4.047A pdb=" N ILE B1054 " --> pdb=" O PRO B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1104 Processing helix chain 'B' and resid 1105 through 1117 Processing helix chain 'B' and resid 1118 through 1143 removed outlier: 4.576A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B1143 " --> pdb=" O THR B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1150 Processing helix chain 'B' and resid 1151 through 1164 removed outlier: 3.615A pdb=" N ILE B1159 " --> pdb=" O HIS B1155 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS B1164 " --> pdb=" O PHE B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 removed outlier: 3.556A pdb=" N PHE B1205 " --> pdb=" O ILE B1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 1215 through 1240 removed outlier: 3.609A pdb=" N THR B1223 " --> pdb=" O ARG B1219 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'C' and resid 201 through 216 removed outlier: 3.848A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.577A pdb=" N HIS C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'C' and resid 279 through 283 removed outlier: 4.025A pdb=" N LYS C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.856A pdb=" N ILE C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.764A pdb=" N LYS C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 402 removed outlier: 3.524A pdb=" N THR C 402 " --> pdb=" O ILE C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 439 through 453 removed outlier: 3.566A pdb=" N LEU C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 466 Processing helix chain 'C' and resid 469 through 475 Processing helix chain 'C' and resid 486 through 498 Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 536 through 545 removed outlier: 3.611A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 545 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.711A pdb=" N GLY C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.980A pdb=" N ASN C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 648 removed outlier: 4.339A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.884A pdb=" N GLN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 Processing helix chain 'C' and resid 690 through 717 Processing helix chain 'C' and resid 717 through 725 Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 746 through 751 Processing helix chain 'C' and resid 752 through 765 removed outlier: 3.757A pdb=" N GLY C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 783 Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 862 through 866 removed outlier: 3.876A pdb=" N GLU C 866 " --> pdb=" O ARG C 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 862 through 866' Processing helix chain 'C' and resid 867 through 869 No H-bonds generated for 'chain 'C' and resid 867 through 869' Processing helix chain 'C' and resid 870 through 893 removed outlier: 3.606A pdb=" N TYR C 891 " --> pdb=" O MET C 887 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 892 " --> pdb=" O LEU C 888 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL C 893 " --> pdb=" O PHE C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 925 Processing helix chain 'C' and resid 930 through 939 removed outlier: 3.821A pdb=" N LYS C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 962 removed outlier: 3.678A pdb=" N VAL C 945 " --> pdb=" O GLU C 941 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 962 " --> pdb=" O MET C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 985 Processing helix chain 'C' and resid 985 through 991 removed outlier: 4.158A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1033 removed outlier: 3.826A pdb=" N ILE C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE C1015 " --> pdb=" O AMET C1011 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1046 removed outlier: 3.694A pdb=" N ILE C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1054 removed outlier: 4.144A pdb=" N ILE C1054 " --> pdb=" O PRO C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1104 removed outlier: 4.383A pdb=" N ALA C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1117 Processing helix chain 'C' and resid 1118 through 1143 removed outlier: 4.579A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG C1143 " --> pdb=" O THR C1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1150 Processing helix chain 'C' and resid 1151 through 1164 removed outlier: 3.616A pdb=" N ILE C1159 " --> pdb=" O HIS C1155 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C1160 " --> pdb=" O MET C1156 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS C1164 " --> pdb=" O PHE C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1214 Processing helix chain 'C' and resid 1215 through 1240 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.841A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.796A pdb=" N HIS D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 279 through 283 removed outlier: 4.085A pdb=" N LYS D 283 " --> pdb=" O PRO D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.653A pdb=" N LEU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.823A pdb=" N ILE D 346 " --> pdb=" O GLY D 342 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.976A pdb=" N LYS D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.556A pdb=" N THR D 402 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 439 through 451 removed outlier: 3.556A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 466 Processing helix chain 'D' and resid 469 through 475 Processing helix chain 'D' and resid 486 through 498 Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 528 removed outlier: 3.643A pdb=" N ASN D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 544 removed outlier: 3.669A pdb=" N LEU D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.704A pdb=" N GLY D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 587 removed outlier: 3.981A pdb=" N ASN D 587 " --> pdb=" O THR D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 648 removed outlier: 4.340A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 3.894A pdb=" N GLN D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 685 Processing helix chain 'D' and resid 690 through 717 Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 746 through 751 Processing helix chain 'D' and resid 752 through 764 Processing helix chain 'D' and resid 774 through 783 Processing helix chain 'D' and resid 862 through 866 removed outlier: 3.871A pdb=" N GLU D 866 " --> pdb=" O ARG D 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 862 through 866' Processing helix chain 'D' and resid 867 through 869 No H-bonds generated for 'chain 'D' and resid 867 through 869' Processing helix chain 'D' and resid 870 through 893 removed outlier: 3.620A pdb=" N TYR D 891 " --> pdb=" O MET D 887 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 892 " --> pdb=" O LEU D 888 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D 893 " --> pdb=" O PHE D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 925 Processing helix chain 'D' and resid 930 through 939 removed outlier: 3.774A pdb=" N LYS D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 962 removed outlier: 3.689A pdb=" N VAL D 945 " --> pdb=" O GLU D 941 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 962 " --> pdb=" O MET D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 985 removed outlier: 4.319A pdb=" N ILE D 980 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 3.837A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 996 through 1033 removed outlier: 3.922A pdb=" N ILE D1008 " --> pdb=" O GLY D1004 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR D1012 " --> pdb=" O ILE D1008 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE D1013 " --> pdb=" O ASP D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1046 removed outlier: 3.892A pdb=" N ILE D1046 " --> pdb=" O LEU D1042 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1054 removed outlier: 3.927A pdb=" N ILE D1054 " --> pdb=" O PRO D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1090 through 1104 Processing helix chain 'D' and resid 1105 through 1117 Processing helix chain 'D' and resid 1118 through 1143 removed outlier: 4.579A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D1143 " --> pdb=" O THR D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1150 Processing helix chain 'D' and resid 1151 through 1164 removed outlier: 3.668A pdb=" N ILE D1159 " --> pdb=" O HIS D1155 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D1160 " --> pdb=" O MET D1156 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS D1164 " --> pdb=" O PHE D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 removed outlier: 3.600A pdb=" N THR D1223 " --> pdb=" O ARG D1219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.543A pdb=" N UNK E 10 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 255 removed outlier: 3.590A pdb=" N TYR A 157 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL A 270 " --> pdb=" O PHE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 189 removed outlier: 6.205A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.543A pdb=" N UNK F 10 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 255 removed outlier: 6.468A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL B 158 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 157 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL B 270 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 186 removed outlier: 5.874A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL B 362 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA B 336 " --> pdb=" O VAL B 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.542A pdb=" N UNK G 10 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 251 through 255 removed outlier: 6.510A pdb=" N GLY C 252 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ALA C 297 " --> pdb=" O GLY C 252 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA C 254 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 158 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR C 157 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL C 270 " --> pdb=" O PHE C 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 187 through 189 removed outlier: 6.259A pdb=" N SER C 187 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.546A pdb=" N UNK H 10 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 255 removed outlier: 6.490A pdb=" N GLY D 252 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA D 297 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA D 254 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL D 158 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR D 157 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL D 270 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.824A pdb=" N ILE D 186 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU D 185 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU D 337 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER D 187 " --> pdb=" O LEU D 337 " (cutoff:3.500A) 1683 hydrogen bonds defined for protein. 5001 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: 7.17 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 16 1.05 - 1.26: 5064 1.26 - 1.47: 13038 1.47 - 1.69: 14422 1.69 - 1.90: 428 Bond restraints: 32968 Sorted by residual: bond pdb=" C03 9Z9 B1402 " pdb=" C74 9Z9 B1402 " ideal model delta sigma weight residual 1.534 0.834 0.700 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C03 9Z9 C1402 " pdb=" C74 9Z9 C1402 " ideal model delta sigma weight residual 1.534 0.835 0.699 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C03 9Z9 A1402 " pdb=" C74 9Z9 A1402 " ideal model delta sigma weight residual 1.534 0.836 0.698 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C03 9Z9 D1402 " pdb=" C74 9Z9 D1402 " ideal model delta sigma weight residual 1.534 0.836 0.698 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C02 9Z9 A1402 " pdb=" C03 9Z9 A1402 " ideal model delta sigma weight residual 1.544 1.012 0.532 2.00e-02 2.50e+03 7.08e+02 ... (remaining 32963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.37: 44556 10.37 - 20.74: 12 20.74 - 31.11: 8 31.11 - 41.48: 4 41.48 - 51.85: 4 Bond angle restraints: 44584 Sorted by residual: angle pdb=" C74 9Z9 D1402 " pdb=" C73 9Z9 D1402 " pdb=" C76 9Z9 D1402 " ideal model delta sigma weight residual 114.05 165.90 -51.85 3.00e+00 1.11e-01 2.99e+02 angle pdb=" C74 9Z9 B1402 " pdb=" C73 9Z9 B1402 " pdb=" C76 9Z9 B1402 " ideal model delta sigma weight residual 114.05 165.89 -51.84 3.00e+00 1.11e-01 2.99e+02 angle pdb=" C74 9Z9 A1402 " pdb=" C73 9Z9 A1402 " pdb=" C76 9Z9 A1402 " ideal model delta sigma weight residual 114.05 165.86 -51.81 3.00e+00 1.11e-01 2.98e+02 angle pdb=" C74 9Z9 C1402 " pdb=" C73 9Z9 C1402 " pdb=" C76 9Z9 C1402 " ideal model delta sigma weight residual 114.05 165.84 -51.79 3.00e+00 1.11e-01 2.98e+02 angle pdb=" C76 9Z9 B1402 " pdb=" C73 9Z9 B1402 " pdb=" O72 9Z9 B1402 " ideal model delta sigma weight residual 109.02 71.26 37.76 3.00e+00 1.11e-01 1.58e+02 ... (remaining 44579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 18555 21.59 - 43.17: 933 43.17 - 64.76: 155 64.76 - 86.34: 7 86.34 - 107.93: 4 Dihedral angle restraints: 19654 sinusoidal: 8162 harmonic: 11492 Sorted by residual: dihedral pdb=" CA THR D 356 " pdb=" C THR D 356 " pdb=" N PRO D 357 " pdb=" CA PRO D 357 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA THR C 356 " pdb=" C THR C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta harmonic sigma weight residual 180.00 159.07 20.93 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 19651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.382: 4968 0.382 - 0.763: 4 0.763 - 1.145: 4 1.145 - 1.527: 0 1.527 - 1.908: 4 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C03 9Z9 B1402 " pdb=" C02 9Z9 B1402 " pdb=" C04 9Z9 B1402 " pdb=" C74 9Z9 B1402 " both_signs ideal model delta sigma weight residual False 2.78 0.87 1.91 2.00e-01 2.50e+01 9.10e+01 chirality pdb=" C03 9Z9 D1402 " pdb=" C02 9Z9 D1402 " pdb=" C04 9Z9 D1402 " pdb=" C74 9Z9 D1402 " both_signs ideal model delta sigma weight residual False 2.78 0.87 1.91 2.00e-01 2.50e+01 9.10e+01 chirality pdb=" C03 9Z9 A1402 " pdb=" C02 9Z9 A1402 " pdb=" C04 9Z9 A1402 " pdb=" C74 9Z9 A1402 " both_signs ideal model delta sigma weight residual False 2.78 0.87 1.91 2.00e-01 2.50e+01 9.09e+01 ... (remaining 4977 not shown) Planarity restraints: 5516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 784 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO C 785 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 785 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 785 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D1147 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.35e+00 pdb=" N PRO D1148 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D1148 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D1148 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 997 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO D 998 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 998 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 998 " -0.029 5.00e-02 4.00e+02 ... (remaining 5513 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7400 2.79 - 3.31: 31105 3.31 - 3.84: 50401 3.84 - 4.37: 55618 4.37 - 4.90: 99316 Nonbonded interactions: 243840 Sorted by model distance: nonbonded pdb=" OG SER B 187 " pdb=" OE2 GLU B 316 " model vdw 2.258 3.040 nonbonded pdb=" O SER A 292 " pdb=" ND1 HIS A 293 " model vdw 2.270 3.120 nonbonded pdb=" ND2 ASN B 890 " pdb=" OH TYR B 983 " model vdw 2.290 3.120 nonbonded pdb=" ND2 ASN D 890 " pdb=" OH TYR D 983 " model vdw 2.291 3.120 nonbonded pdb=" OE2 GLU B 489 " pdb=" NH1 ARG B 522 " model vdw 2.304 3.120 ... (remaining 243835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 129 through 1403) selection = (chain 'B' and resid 129 through 1403) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 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: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.110 Set scattering table: 0.050 Process input model: 30.300 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.015 0.700 32968 Z= 0.755 Angle : 1.015 51.853 44584 Z= 0.395 Chirality : 0.075 1.908 4980 Planarity : 0.004 0.053 5516 Dihedral : 12.700 107.929 12222 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.61 % Allowed : 6.64 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3824 helix: 1.02 (0.11), residues: 2404 sheet: -1.62 (0.36), residues: 232 loop : -1.61 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 231 TYR 0.013 0.001 TYR A1048 PHE 0.009 0.001 PHE A1140 TRP 0.014 0.001 TRP A 763 HIS 0.004 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.01520 / 0.75 (32968) covalent geometry : angle 1.01479 / 0.39 (44584) hydrogen bonds : bond 0.15595 / 10.38 ( 1683) hydrogen bonds : angle 5.24894 / 3.64 ( 5001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 622 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8409 (mtp-110) cc_final: 0.8053 (ttm110) REVERT: A 584 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8517 (tt) REVERT: A 653 MET cc_start: 0.8411 (ttm) cc_final: 0.8071 (ttm) REVERT: A 862 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.4528 (ptt-90) REVERT: A 948 LEU cc_start: 0.8573 (tp) cc_final: 0.8214 (tp) REVERT: A 958 MET cc_start: 0.8386 (tmm) cc_final: 0.7946 (tmm) REVERT: A 979 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8531 (tp) REVERT: A 1022 MET cc_start: 0.7386 (mmt) cc_final: 0.7149 (mmt) REVERT: A 1203 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7963 (tm-30) REVERT: A 1228 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 240 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7067 (t70) REVERT: B 290 MET cc_start: 0.8377 (mmm) cc_final: 0.7970 (mmm) REVERT: B 352 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8594 (m-10) REVERT: B 354 ARG cc_start: 0.8337 (mtp-110) cc_final: 0.8036 (ttm110) REVERT: B 418 MET cc_start: 0.8042 (mmm) cc_final: 0.7836 (mmm) REVERT: B 687 MET cc_start: 0.6606 (mmt) cc_final: 0.6366 (mmt) REVERT: B 689 ASP cc_start: 0.6677 (m-30) cc_final: 0.6374 (t0) REVERT: B 862 ARG cc_start: 0.5710 (OUTLIER) cc_final: 0.3720 (pmt-80) REVERT: B 936 LYS cc_start: 0.8110 (ptmm) cc_final: 0.7806 (mmtp) REVERT: B 958 MET cc_start: 0.8249 (tmm) cc_final: 0.7947 (tmm) REVERT: B 1022 MET cc_start: 0.7473 (mmt) cc_final: 0.7253 (mmt) REVERT: B 1228 GLU cc_start: 0.7738 (tp30) cc_final: 0.7319 (tm-30) REVERT: C 238 LYS cc_start: 0.8298 (mmtp) cc_final: 0.8058 (mmtp) REVERT: C 352 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.8412 (m-10) REVERT: C 354 ARG cc_start: 0.8287 (mtp-110) cc_final: 0.8028 (ttm110) REVERT: C 653 MET cc_start: 0.8436 (ttm) cc_final: 0.8092 (ttm) REVERT: C 687 MET cc_start: 0.6741 (mmt) cc_final: 0.6506 (mmt) REVERT: C 862 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.4514 (ptt-90) REVERT: C 936 LYS cc_start: 0.8230 (ptmm) cc_final: 0.7868 (mmtp) REVERT: C 958 MET cc_start: 0.8361 (tmm) cc_final: 0.7982 (tmm) REVERT: C 979 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8470 (tp) REVERT: C 1228 GLU cc_start: 0.7753 (tp30) cc_final: 0.7370 (tm-30) REVERT: D 687 MET cc_start: 0.6625 (mmt) cc_final: 0.6264 (mmp) REVERT: D 862 ARG cc_start: 0.5760 (OUTLIER) cc_final: 0.4467 (ptt-90) REVERT: D 936 LYS cc_start: 0.8189 (ptmm) cc_final: 0.7807 (mmtp) REVERT: D 958 MET cc_start: 0.8309 (tmm) cc_final: 0.7936 (tmm) REVERT: D 1022 MET cc_start: 0.7530 (mmt) cc_final: 0.7284 (mmt) REVERT: D 1062 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.7003 (mp10) REVERT: D 1228 GLU cc_start: 0.7730 (tp30) cc_final: 0.7342 (tm-30) outliers start: 124 outliers final: 43 residues processed: 723 average time/residue: 0.1779 time to fit residues: 208.4892 Evaluate side-chains 526 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 472 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 862 ARG Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 352 TYR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 862 ARG Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1146 LEU Chi-restraints excluded: chain C residue 1217 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 862 ARG Chi-restraints excluded: chain D residue 1062 GLN Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1217 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 HIS A 261 ASN A 262 GLN A 275 GLN A 314 GLN A 318 HIS A 378 HIS A 411 GLN A 632 ASN A 697 HIS A 890 ASN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN A1115 ASN A1161 GLN B 232 HIS B 261 ASN B 262 GLN B 275 GLN B 314 GLN B 318 HIS B 378 HIS B 411 GLN B 632 ASN B 659 GLN B 697 HIS B 890 ASN B1029 GLN B1115 ASN B1161 GLN B1229 ASN C 232 HIS C 261 ASN C 262 GLN C 275 GLN C 314 GLN C 318 HIS C 411 GLN C 539 HIS C 632 ASN C 697 HIS C 890 ASN C1115 ASN C1238 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 HIS D 261 ASN D 262 GLN D 275 GLN D 314 GLN D 318 HIS D 378 HIS D 411 GLN D 632 ASN D 697 HIS D 890 ASN D 978 ASN D1029 GLN D1115 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114970 restraints weight = 50818.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118657 restraints weight = 30149.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121127 restraints weight = 21528.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122748 restraints weight = 17276.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123667 restraints weight = 14895.868| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32968 Z= 0.188 Angle : 0.579 7.912 44584 Z= 0.295 Chirality : 0.040 0.146 4980 Planarity : 0.005 0.054 5516 Dihedral : 8.923 98.066 4600 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.06 % Allowed : 11.33 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3824 helix: 1.24 (0.11), residues: 2432 sheet: -1.73 (0.35), residues: 224 loop : -1.64 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1211 TYR 0.016 0.001 TYR D 479 PHE 0.022 0.001 PHE A1059 TRP 0.016 0.001 TRP A 763 HIS 0.010 0.001 HIS D 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (32968) covalent geometry : angle 0.57897 / 0.29 (44584) hydrogen bonds : bond 0.05393 / 3.64 ( 1683) hydrogen bonds : angle 3.98518 / 2.81 ( 5001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 469 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.7997 (mmm) cc_final: 0.7796 (tpp) REVERT: A 354 ARG cc_start: 0.8555 (mtp-110) cc_final: 0.8195 (ttm110) REVERT: A 584 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8502 (tt) REVERT: A 862 ARG cc_start: 0.5687 (OUTLIER) cc_final: 0.3659 (pmt-80) REVERT: A 936 LYS cc_start: 0.8283 (ptmm) cc_final: 0.8000 (mmtp) REVERT: A 958 MET cc_start: 0.8413 (tmm) cc_final: 0.8041 (tmm) REVERT: A 979 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8511 (tp) REVERT: A 983 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.6751 (t80) REVERT: A 1022 MET cc_start: 0.7444 (mmt) cc_final: 0.7199 (mmt) REVERT: A 1142 GLU cc_start: 0.7319 (tm-30) cc_final: 0.7006 (tm-30) REVERT: A 1203 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8067 (tm-30) REVERT: B 240 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7028 (t70) REVERT: B 352 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8601 (m-10) REVERT: B 354 ARG cc_start: 0.8485 (mtp-110) cc_final: 0.8113 (ttm110) REVERT: B 418 MET cc_start: 0.8017 (mmm) cc_final: 0.7808 (mmm) REVERT: B 687 MET cc_start: 0.6689 (mmt) cc_final: 0.6481 (mmt) REVERT: B 862 ARG cc_start: 0.5702 (OUTLIER) cc_final: 0.3649 (pmt-80) REVERT: B 936 LYS cc_start: 0.8281 (ptmm) cc_final: 0.8009 (mmtp) REVERT: B 958 MET cc_start: 0.8278 (tmm) cc_final: 0.8051 (ttp) REVERT: B 983 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.7031 (t80) REVERT: B 1010 MET cc_start: 0.7470 (ttp) cc_final: 0.7153 (ttm) REVERT: B 1022 MET cc_start: 0.7506 (mmt) cc_final: 0.7291 (mmt) REVERT: B 1142 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 1228 GLU cc_start: 0.8031 (tp30) cc_final: 0.7647 (tm-30) REVERT: B 1233 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7468 (mmp80) REVERT: C 235 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: C 238 LYS cc_start: 0.8380 (mmtp) cc_final: 0.8129 (mmtp) REVERT: C 354 ARG cc_start: 0.8487 (mtp-110) cc_final: 0.8233 (ttm110) REVERT: C 687 MET cc_start: 0.6770 (mmt) cc_final: 0.6343 (mmp) REVERT: C 862 ARG cc_start: 0.5741 (OUTLIER) cc_final: 0.3702 (pmt-80) REVERT: C 958 MET cc_start: 0.8330 (tmm) cc_final: 0.8048 (ttp) REVERT: C 979 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8495 (tp) REVERT: C 983 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.6751 (t80) REVERT: C 1142 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6951 (tm-30) REVERT: C 1228 GLU cc_start: 0.8072 (tp30) cc_final: 0.7805 (tm-30) REVERT: C 1233 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7621 (mmp80) REVERT: C 1236 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8473 (mm-30) REVERT: D 240 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7827 (t-90) REVERT: D 292 SER cc_start: 0.8686 (t) cc_final: 0.8377 (t) REVERT: D 348 ILE cc_start: 0.8527 (pt) cc_final: 0.8290 (pt) REVERT: D 687 MET cc_start: 0.6624 (mmt) cc_final: 0.6282 (mmp) REVERT: D 862 ARG cc_start: 0.5718 (OUTLIER) cc_final: 0.3675 (pmt-80) REVERT: D 958 MET cc_start: 0.8340 (tmm) cc_final: 0.8002 (tmm) REVERT: D 983 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7020 (t80) REVERT: D 1022 MET cc_start: 0.7534 (mmt) cc_final: 0.7283 (mmt) REVERT: D 1142 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6957 (tm-30) REVERT: D 1228 GLU cc_start: 0.7972 (tp30) cc_final: 0.7604 (tm-30) REVERT: D 1232 MET cc_start: 0.8706 (tpp) cc_final: 0.8438 (tpp) outliers start: 105 outliers final: 60 residues processed: 546 average time/residue: 0.1709 time to fit residues: 154.2040 Evaluate side-chains 525 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 450 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 862 ARG Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 862 ARG Chi-restraints excluded: chain C residue 955 SER Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1146 LEU Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 862 ARG Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1150 LEU Chi-restraints excluded: chain D residue 1230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 70 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 195 optimal weight: 4.9990 chunk 343 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 332 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1229 ASN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1029 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1229 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113554 restraints weight = 50227.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117359 restraints weight = 29393.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119895 restraints weight = 20885.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.121585 restraints weight = 16713.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122587 restraints weight = 14382.014| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32968 Z= 0.127 Angle : 0.521 8.630 44584 Z= 0.263 Chirality : 0.039 0.156 4980 Planarity : 0.004 0.054 5516 Dihedral : 8.377 84.840 4565 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.85 % Allowed : 12.70 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3824 helix: 1.39 (0.11), residues: 2440 sheet: -1.74 (0.35), residues: 224 loop : -1.54 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1206 TYR 0.014 0.001 TYR C 981 PHE 0.023 0.001 PHE D1059 TRP 0.014 0.001 TRP A 763 HIS 0.009 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (32968) covalent geometry : angle 0.52059 / 0.26 (44584) hydrogen bonds : bond 0.04619 / 3.12 ( 1683) hydrogen bonds : angle 3.70315 / 2.62 ( 5001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 477 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7158 (t-90) REVERT: A 354 ARG cc_start: 0.8491 (mtp-110) cc_final: 0.8146 (ttm110) REVERT: A 568 MET cc_start: 0.8675 (tpt) cc_final: 0.8349 (tpt) REVERT: A 584 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8498 (tt) REVERT: A 862 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.3729 (pmt-80) REVERT: A 890 ASN cc_start: 0.9351 (OUTLIER) cc_final: 0.9114 (m-40) REVERT: A 936 LYS cc_start: 0.8264 (ptmm) cc_final: 0.7990 (mmtp) REVERT: A 958 MET cc_start: 0.8327 (tmm) cc_final: 0.8014 (ttp) REVERT: A 979 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8534 (tp) REVERT: A 983 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.6806 (t80) REVERT: A 1022 MET cc_start: 0.7322 (mmt) cc_final: 0.7109 (mmt) REVERT: A 1142 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6922 (tm-30) REVERT: A 1203 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 240 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.6912 (t70) REVERT: B 352 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8496 (m-10) REVERT: B 354 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.8180 (ttm110) REVERT: B 568 MET cc_start: 0.8639 (tpt) cc_final: 0.8334 (tpt) REVERT: B 687 MET cc_start: 0.6644 (mmt) cc_final: 0.6441 (mmp) REVERT: B 862 ARG cc_start: 0.5781 (OUTLIER) cc_final: 0.3728 (pmt-80) REVERT: B 936 LYS cc_start: 0.8275 (ptmm) cc_final: 0.8019 (mmtp) REVERT: B 958 MET cc_start: 0.8238 (tmm) cc_final: 0.7994 (ttp) REVERT: B 983 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.6877 (t80) REVERT: B 1002 MET cc_start: 0.7330 (mmm) cc_final: 0.6813 (mtt) REVERT: B 1022 MET cc_start: 0.7365 (mmt) cc_final: 0.7139 (mmt) REVERT: B 1142 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6888 (tm-30) REVERT: B 1233 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7567 (mmp80) REVERT: C 235 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: C 238 LYS cc_start: 0.8356 (mmtp) cc_final: 0.8086 (mmtp) REVERT: C 240 HIS cc_start: 0.7833 (OUTLIER) cc_final: 0.7329 (t-90) REVERT: C 354 ARG cc_start: 0.8457 (mtp-110) cc_final: 0.8167 (ttm110) REVERT: C 568 MET cc_start: 0.8652 (tpt) cc_final: 0.8344 (tpt) REVERT: C 687 MET cc_start: 0.6822 (mmt) cc_final: 0.6332 (mmp) REVERT: C 862 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.3753 (pmt-80) REVERT: C 890 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.9124 (m-40) REVERT: C 936 LYS cc_start: 0.8291 (ptmm) cc_final: 0.7933 (mmtp) REVERT: C 958 MET cc_start: 0.8206 (tmm) cc_final: 0.7977 (ttp) REVERT: C 979 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8455 (tp) REVERT: C 983 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.6795 (t80) REVERT: C 1002 MET cc_start: 0.7705 (mmt) cc_final: 0.7283 (mmt) REVERT: C 1142 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6863 (tm-30) REVERT: C 1203 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7896 (tm-30) REVERT: C 1228 GLU cc_start: 0.7968 (tp30) cc_final: 0.7682 (tp30) REVERT: D 240 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7090 (t-90) REVERT: D 568 MET cc_start: 0.8685 (tpt) cc_final: 0.8386 (tpt) REVERT: D 687 MET cc_start: 0.6781 (mmt) cc_final: 0.6360 (mmp) REVERT: D 862 ARG cc_start: 0.5796 (OUTLIER) cc_final: 0.3745 (pmt-80) REVERT: D 958 MET cc_start: 0.8298 (tmm) cc_final: 0.7915 (tmm) REVERT: D 983 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.6881 (t80) REVERT: D 1007 MET cc_start: 0.7545 (mtp) cc_final: 0.7324 (mtp) REVERT: D 1022 MET cc_start: 0.7400 (mmt) cc_final: 0.7149 (mmt) REVERT: D 1142 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6906 (tm-30) REVERT: D 1203 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7801 (tm-30) REVERT: D 1228 GLU cc_start: 0.7855 (tp30) cc_final: 0.7488 (tm-30) outliers start: 98 outliers final: 50 residues processed: 547 average time/residue: 0.1709 time to fit residues: 153.7870 Evaluate side-chains 508 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 439 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 862 ARG Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 862 ARG Chi-restraints excluded: chain C residue 890 ASN Chi-restraints excluded: chain C residue 955 SER Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1146 LEU Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 862 ARG Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1150 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 67 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 187 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 147 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 GLN B 890 ASN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1199 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1229 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 GLN D 890 ASN D1238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.108323 restraints weight = 50843.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112010 restraints weight = 30094.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.114502 restraints weight = 21663.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116161 restraints weight = 17458.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117252 restraints weight = 15115.118| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 32968 Z= 0.246 Angle : 0.614 6.980 44584 Z= 0.311 Chirality : 0.042 0.142 4980 Planarity : 0.005 0.073 5516 Dihedral : 8.245 74.459 4554 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.61 % Allowed : 13.95 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3824 helix: 1.29 (0.11), residues: 2428 sheet: -1.71 (0.35), residues: 232 loop : -1.55 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1233 TYR 0.013 0.001 TYR A1048 PHE 0.028 0.001 PHE A1059 TRP 0.018 0.001 TRP A 763 HIS 0.011 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.25 (32968) covalent geometry : angle 0.61404 / 0.31 (44584) hydrogen bonds : bond 0.05528 / 3.72 ( 1683) hydrogen bonds : angle 3.97675 / 2.82 ( 5001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 447 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7327 (t-90) REVERT: A 354 ARG cc_start: 0.8580 (mtp-110) cc_final: 0.8196 (ttm110) REVERT: A 568 MET cc_start: 0.8828 (tpt) cc_final: 0.8421 (tpt) REVERT: A 862 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.3790 (pmt-80) REVERT: A 936 LYS cc_start: 0.8319 (ptmm) cc_final: 0.8026 (mmtp) REVERT: A 958 MET cc_start: 0.8363 (tmm) cc_final: 0.8119 (ttp) REVERT: A 979 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8619 (tp) REVERT: A 983 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.6849 (t80) REVERT: A 1022 MET cc_start: 0.7360 (mmt) cc_final: 0.7159 (mmt) REVERT: A 1053 MET cc_start: 0.8289 (ttm) cc_final: 0.8019 (ttm) REVERT: A 1116 ASN cc_start: 0.8466 (m-40) cc_final: 0.8069 (m-40) REVERT: A 1142 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7037 (tm-30) REVERT: A 1203 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 240 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7240 (t70) REVERT: B 352 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.8715 (m-10) REVERT: B 354 ARG cc_start: 0.8522 (mtp-110) cc_final: 0.8210 (ttm110) REVERT: B 568 MET cc_start: 0.8807 (tpt) cc_final: 0.8408 (tpt) REVERT: B 687 MET cc_start: 0.6597 (mmt) cc_final: 0.6124 (mmp) REVERT: B 862 ARG cc_start: 0.5756 (OUTLIER) cc_final: 0.3752 (pmt-80) REVERT: B 936 LYS cc_start: 0.8329 (ptmm) cc_final: 0.8044 (mmtp) REVERT: B 958 MET cc_start: 0.8351 (tmm) cc_final: 0.8149 (ttp) REVERT: B 983 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.7100 (t80) REVERT: B 1002 MET cc_start: 0.7617 (mmm) cc_final: 0.7076 (mtt) REVERT: B 1010 MET cc_start: 0.7559 (ttp) cc_final: 0.7281 (ttm) REVERT: B 1022 MET cc_start: 0.7508 (mmt) cc_final: 0.7300 (mmt) REVERT: B 1142 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6938 (tm-30) REVERT: B 1203 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7916 (tm-30) REVERT: C 235 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7992 (m-30) REVERT: C 238 LYS cc_start: 0.8432 (mmtp) cc_final: 0.8175 (mmmm) REVERT: C 240 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7689 (t-90) REVERT: C 354 ARG cc_start: 0.8519 (mtp-110) cc_final: 0.8159 (ttm110) REVERT: C 568 MET cc_start: 0.8801 (tpt) cc_final: 0.8461 (tpt) REVERT: C 687 MET cc_start: 0.6829 (mmt) cc_final: 0.6416 (mmp) REVERT: C 862 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.3812 (pmt-80) REVERT: C 936 LYS cc_start: 0.8146 (ptmm) cc_final: 0.7867 (mmtp) REVERT: C 958 MET cc_start: 0.8317 (tmm) cc_final: 0.8116 (ttp) REVERT: C 979 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8546 (tp) REVERT: C 983 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.6843 (t80) REVERT: C 1002 MET cc_start: 0.7937 (mmt) cc_final: 0.7718 (mmt) REVERT: C 1116 ASN cc_start: 0.8438 (m-40) cc_final: 0.8068 (m-40) REVERT: C 1142 GLU cc_start: 0.7274 (tm-30) cc_final: 0.7045 (tm-30) REVERT: C 1203 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8090 (tm-30) REVERT: C 1228 GLU cc_start: 0.8059 (tp30) cc_final: 0.7847 (tp30) REVERT: D 240 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7460 (t-90) REVERT: D 292 SER cc_start: 0.8761 (t) cc_final: 0.8466 (t) REVERT: D 568 MET cc_start: 0.8824 (tpt) cc_final: 0.8435 (tpt) REVERT: D 687 MET cc_start: 0.6728 (mmt) cc_final: 0.6364 (mmp) REVERT: D 862 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.3894 (pmt-80) REVERT: D 936 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7792 (mmtp) REVERT: D 958 MET cc_start: 0.8474 (tmm) cc_final: 0.8137 (ttp) REVERT: D 983 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7131 (t80) REVERT: D 1142 GLU cc_start: 0.7273 (tm-30) cc_final: 0.7039 (tm-30) REVERT: D 1203 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7975 (tm-30) REVERT: D 1228 GLU cc_start: 0.8086 (tp30) cc_final: 0.7746 (tm-30) outliers start: 124 outliers final: 68 residues processed: 537 average time/residue: 0.1684 time to fit residues: 149.5693 Evaluate side-chains 506 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 422 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 862 ARG Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 862 ARG Chi-restraints excluded: chain C residue 883 ILE Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1146 LEU Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 665 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 862 ARG Chi-restraints excluded: chain D residue 883 ILE Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1150 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 242 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 338 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 375 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 284 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN B1115 ASN B1116 ASN C 890 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN D1116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112859 restraints weight = 50267.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116697 restraints weight = 29340.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119288 restraints weight = 20850.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121022 restraints weight = 16668.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122126 restraints weight = 14297.657| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32968 Z= 0.123 Angle : 0.521 7.465 44584 Z= 0.262 Chirality : 0.039 0.142 4980 Planarity : 0.004 0.073 5516 Dihedral : 7.899 65.141 4551 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.94 % Allowed : 15.14 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3824 helix: 1.53 (0.11), residues: 2436 sheet: -1.73 (0.34), residues: 232 loop : -1.55 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1206 TYR 0.015 0.001 TYR C 981 PHE 0.022 0.001 PHE A1059 TRP 0.014 0.001 TRP A 763 HIS 0.010 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (32968) covalent geometry : angle 0.52080 / 0.26 (44584) hydrogen bonds : bond 0.04551 / 3.08 ( 1683) hydrogen bonds : angle 3.63157 / 2.58 ( 5001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 466 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7447 (t-90) REVERT: A 354 ARG cc_start: 0.8585 (mtp-110) cc_final: 0.8207 (ttm110) REVERT: A 568 MET cc_start: 0.8806 (tpt) cc_final: 0.8484 (tpt) REVERT: A 584 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8509 (tt) REVERT: A 862 ARG cc_start: 0.5717 (OUTLIER) cc_final: 0.3633 (pmt-80) REVERT: A 936 LYS cc_start: 0.8241 (ptmm) cc_final: 0.7917 (mmtp) REVERT: A 958 MET cc_start: 0.8271 (tmm) cc_final: 0.8027 (ttp) REVERT: A 979 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8552 (tp) REVERT: A 983 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.6524 (t80) REVERT: A 1022 MET cc_start: 0.7410 (mmt) cc_final: 0.7200 (mmt) REVERT: A 1142 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6985 (tm-30) REVERT: A 1203 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 1233 ARG cc_start: 0.8108 (tpp80) cc_final: 0.7607 (tpp80) REVERT: B 240 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7144 (t70) REVERT: B 248 ILE cc_start: 0.8897 (mm) cc_final: 0.8677 (mm) REVERT: B 352 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8467 (m-10) REVERT: B 354 ARG cc_start: 0.8552 (mtp-110) cc_final: 0.8077 (ttm110) REVERT: B 568 MET cc_start: 0.8789 (tpt) cc_final: 0.8474 (tpt) REVERT: B 862 ARG cc_start: 0.5734 (OUTLIER) cc_final: 0.3652 (pmt-80) REVERT: B 936 LYS cc_start: 0.8273 (ptmm) cc_final: 0.7985 (mmtp) REVERT: B 958 MET cc_start: 0.8259 (tmm) cc_final: 0.8046 (ttp) REVERT: B 983 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.6977 (t80) REVERT: B 1002 MET cc_start: 0.7493 (mmm) cc_final: 0.6913 (mtt) REVERT: B 1010 MET cc_start: 0.7348 (ttp) cc_final: 0.7106 (ttm) REVERT: B 1022 MET cc_start: 0.7516 (mmt) cc_final: 0.7315 (mmt) REVERT: B 1142 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6941 (tm-30) REVERT: B 1203 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7901 (tm-30) REVERT: C 235 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7975 (m-30) REVERT: C 238 LYS cc_start: 0.8432 (mmtp) cc_final: 0.8164 (mmmm) REVERT: C 354 ARG cc_start: 0.8560 (mtp-110) cc_final: 0.8179 (ttm110) REVERT: C 568 MET cc_start: 0.8774 (tpt) cc_final: 0.8456 (tpt) REVERT: C 687 MET cc_start: 0.6817 (mmt) cc_final: 0.6304 (mmp) REVERT: C 862 ARG cc_start: 0.5752 (OUTLIER) cc_final: 0.3662 (pmt-80) REVERT: C 890 ASN cc_start: 0.9438 (OUTLIER) cc_final: 0.9162 (m-40) REVERT: C 936 LYS cc_start: 0.8163 (ptmm) cc_final: 0.7844 (mmtp) REVERT: C 979 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8499 (tp) REVERT: C 983 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.6552 (t80) REVERT: C 1142 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6925 (tm-30) REVERT: C 1203 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8079 (tm-30) REVERT: D 240 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.7064 (t-90) REVERT: D 292 SER cc_start: 0.8714 (t) cc_final: 0.8417 (t) REVERT: D 568 MET cc_start: 0.8794 (tpt) cc_final: 0.8483 (tpt) REVERT: D 687 MET cc_start: 0.6703 (mmt) cc_final: 0.6243 (mmp) REVERT: D 862 ARG cc_start: 0.5736 (OUTLIER) cc_final: 0.3640 (pmt-80) REVERT: D 936 LYS cc_start: 0.8131 (ptmm) cc_final: 0.7732 (mmtp) REVERT: D 958 MET cc_start: 0.8385 (tmm) cc_final: 0.8050 (tmm) REVERT: D 983 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.6925 (t80) REVERT: D 1007 MET cc_start: 0.7665 (mtp) cc_final: 0.7423 (mtp) REVERT: D 1142 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6951 (tm-30) REVERT: D 1203 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7962 (tm-30) outliers start: 101 outliers final: 67 residues processed: 538 average time/residue: 0.1778 time to fit residues: 156.4128 Evaluate side-chains 522 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 438 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 862 ARG Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 862 ARG Chi-restraints excluded: chain C residue 883 ILE Chi-restraints excluded: chain C residue 890 ASN Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1146 LEU Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 665 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 862 ARG Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1150 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 275 optimal weight: 0.0370 chunk 113 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 67 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 359 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 overall best weight: 2.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 ASN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS C 890 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108901 restraints weight = 50541.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112568 restraints weight = 29961.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.115051 restraints weight = 21499.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116671 restraints weight = 17301.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117763 restraints weight = 14987.708| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 32968 Z= 0.228 Angle : 0.601 8.164 44584 Z= 0.303 Chirality : 0.041 0.137 4980 Planarity : 0.004 0.077 5516 Dihedral : 7.964 59.925 4551 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.47 % Allowed : 15.75 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3824 helix: 1.42 (0.11), residues: 2424 sheet: -1.92 (0.34), residues: 236 loop : -1.53 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1206 TYR 0.013 0.001 TYR A1048 PHE 0.026 0.001 PHE A1059 TRP 0.017 0.001 TRP A 763 HIS 0.010 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (32968) covalent geometry : angle 0.60063 / 0.30 (44584) hydrogen bonds : bond 0.05357 / 3.63 ( 1683) hydrogen bonds : angle 3.87786 / 2.75 ( 5001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 429 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7513 (t-90) REVERT: A 354 ARG cc_start: 0.8570 (mtp-110) cc_final: 0.8204 (ttm110) REVERT: A 568 MET cc_start: 0.8830 (tpt) cc_final: 0.8489 (tpt) REVERT: A 584 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8440 (tt) REVERT: A 763 TRP cc_start: 0.9227 (OUTLIER) cc_final: 0.8727 (t-100) REVERT: A 862 ARG cc_start: 0.5844 (OUTLIER) cc_final: 0.3851 (pmt-80) REVERT: A 890 ASN cc_start: 0.9430 (OUTLIER) cc_final: 0.9169 (m-40) REVERT: A 936 LYS cc_start: 0.8264 (ptmm) cc_final: 0.7951 (mmtp) REVERT: A 958 MET cc_start: 0.8312 (tmm) cc_final: 0.8096 (ttp) REVERT: A 979 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8594 (tp) REVERT: A 983 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.6670 (t80) REVERT: A 1002 MET cc_start: 0.7909 (mmt) cc_final: 0.7654 (mmt) REVERT: A 1022 MET cc_start: 0.7398 (mmt) cc_final: 0.7196 (mmt) REVERT: A 1142 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7156 (tm-30) REVERT: A 1203 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 1233 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7605 (tpp80) REVERT: B 240 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7208 (t70) REVERT: B 352 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8684 (m-10) REVERT: B 354 ARG cc_start: 0.8524 (mtp-110) cc_final: 0.8202 (ttm110) REVERT: B 568 MET cc_start: 0.8840 (tpt) cc_final: 0.8493 (tpt) REVERT: B 687 MET cc_start: 0.6274 (mmp) cc_final: 0.5858 (mmp) REVERT: B 763 TRP cc_start: 0.9221 (OUTLIER) cc_final: 0.8745 (t-100) REVERT: B 862 ARG cc_start: 0.5802 (OUTLIER) cc_final: 0.3780 (pmt-80) REVERT: B 936 LYS cc_start: 0.8308 (ptmm) cc_final: 0.8025 (mmtp) REVERT: B 983 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7127 (t80) REVERT: B 1002 MET cc_start: 0.7582 (mmm) cc_final: 0.7011 (mtt) REVERT: B 1010 MET cc_start: 0.7509 (ttp) cc_final: 0.7232 (ttm) REVERT: B 1142 GLU cc_start: 0.7329 (tm-30) cc_final: 0.7070 (tm-30) REVERT: B 1203 GLU cc_start: 0.8231 (tm-30) cc_final: 0.8025 (tm-30) REVERT: C 235 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7959 (m-30) REVERT: C 238 LYS cc_start: 0.8485 (mmtp) cc_final: 0.8197 (mmmm) REVERT: C 354 ARG cc_start: 0.8518 (mtp-110) cc_final: 0.8155 (ttm110) REVERT: C 568 MET cc_start: 0.8809 (tpt) cc_final: 0.8458 (tpt) REVERT: C 687 MET cc_start: 0.6892 (mmt) cc_final: 0.6441 (mmp) REVERT: C 862 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.3872 (pmt-80) REVERT: C 936 LYS cc_start: 0.8171 (ptmm) cc_final: 0.7877 (mmtp) REVERT: C 979 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8522 (tp) REVERT: C 983 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.6777 (t80) REVERT: C 1142 GLU cc_start: 0.7276 (tm-30) cc_final: 0.7040 (tm-30) REVERT: C 1203 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 240 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7192 (t-90) REVERT: D 292 SER cc_start: 0.8766 (t) cc_final: 0.8471 (t) REVERT: D 568 MET cc_start: 0.8831 (tpt) cc_final: 0.8486 (tpt) REVERT: D 687 MET cc_start: 0.6761 (mmt) cc_final: 0.6339 (mmp) REVERT: D 862 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.3901 (pmt-80) REVERT: D 933 GLN cc_start: 0.8326 (tp40) cc_final: 0.7971 (tp40) REVERT: D 936 LYS cc_start: 0.8156 (ptmm) cc_final: 0.7816 (mmtp) REVERT: D 958 MET cc_start: 0.8473 (tmm) cc_final: 0.8147 (ttp) REVERT: D 983 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7137 (t80) REVERT: D 1142 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7119 (tm-30) REVERT: D 1203 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7975 (tm-30) outliers start: 119 outliers final: 89 residues processed: 513 average time/residue: 0.1944 time to fit residues: 164.0643 Evaluate side-chains 522 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 414 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 763 TRP Chi-restraints excluded: chain B residue 862 ARG Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 862 ARG Chi-restraints excluded: chain C residue 883 ILE Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1006 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1146 LEU Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 652 LYS Chi-restraints excluded: chain D residue 665 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 862 ARG Chi-restraints excluded: chain D residue 883 ILE Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1150 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 286 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 329 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 ASN ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.142164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112705 restraints weight = 50244.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.116457 restraints weight = 29839.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118983 restraints weight = 21335.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120670 restraints weight = 17099.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121738 restraints weight = 14727.363| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32968 Z= 0.128 Angle : 0.534 8.929 44584 Z= 0.268 Chirality : 0.038 0.200 4980 Planarity : 0.004 0.075 5516 Dihedral : 7.728 59.514 4551 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.17 % Allowed : 16.66 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3824 helix: 1.56 (0.11), residues: 2448 sheet: -1.90 (0.34), residues: 236 loop : -1.53 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 431 TYR 0.016 0.001 TYR A 981 PHE 0.018 0.001 PHE A1059 TRP 0.013 0.001 TRP A 763 HIS 0.009 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (32968) covalent geometry : angle 0.53361 / 0.27 (44584) hydrogen bonds : bond 0.04554 / 3.09 ( 1683) hydrogen bonds : angle 3.58813 / 2.55 ( 5001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 440 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7625 (t-90) REVERT: A 354 ARG cc_start: 0.8568 (mtp-110) cc_final: 0.8203 (ttm110) REVERT: A 568 MET cc_start: 0.8778 (tpt) cc_final: 0.8461 (tpt) REVERT: A 584 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8466 (tt) REVERT: A 763 TRP cc_start: 0.9169 (OUTLIER) cc_final: 0.8741 (t-100) REVERT: A 770 ARG cc_start: 0.7642 (mmt90) cc_final: 0.7379 (mmt90) REVERT: A 862 ARG cc_start: 0.5750 (OUTLIER) cc_final: 0.3672 (pmt-80) REVERT: A 936 LYS cc_start: 0.8209 (ptmm) cc_final: 0.7899 (mmtp) REVERT: A 958 MET cc_start: 0.8197 (tmm) cc_final: 0.7959 (ttp) REVERT: A 979 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8497 (tp) REVERT: A 983 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.6714 (t80) REVERT: A 1022 MET cc_start: 0.7421 (mmt) cc_final: 0.7214 (mmt) REVERT: A 1142 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6996 (tm-30) REVERT: A 1158 MET cc_start: 0.6222 (tpp) cc_final: 0.5986 (tmm) REVERT: A 1203 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 1233 ARG cc_start: 0.8015 (tpp80) cc_final: 0.7540 (tpp80) REVERT: B 240 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7151 (t70) REVERT: B 352 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8474 (m-10) REVERT: B 354 ARG cc_start: 0.8508 (mtp-110) cc_final: 0.8195 (ttm110) REVERT: B 568 MET cc_start: 0.8762 (tpt) cc_final: 0.8456 (tpt) REVERT: B 862 ARG cc_start: 0.5759 (OUTLIER) cc_final: 0.3686 (pmt-80) REVERT: B 936 LYS cc_start: 0.8289 (ptmm) cc_final: 0.8018 (mmtp) REVERT: B 983 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.6971 (t80) REVERT: B 1002 MET cc_start: 0.7493 (mmm) cc_final: 0.6852 (mtt) REVERT: B 1010 MET cc_start: 0.7316 (ttp) cc_final: 0.7089 (ttm) REVERT: B 1022 MET cc_start: 0.7417 (mmt) cc_final: 0.7187 (mmt) REVERT: B 1142 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6949 (tm-30) REVERT: B 1158 MET cc_start: 0.6212 (tpp) cc_final: 0.6004 (tmm) REVERT: B 1203 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7965 (tm-30) REVERT: C 235 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: C 238 LYS cc_start: 0.8484 (mmtp) cc_final: 0.8196 (mmmm) REVERT: C 354 ARG cc_start: 0.8528 (mtp-110) cc_final: 0.8148 (ttm110) REVERT: C 568 MET cc_start: 0.8754 (tpt) cc_final: 0.8475 (tpt) REVERT: C 687 MET cc_start: 0.6832 (mmt) cc_final: 0.6321 (mmp) REVERT: C 862 ARG cc_start: 0.5790 (OUTLIER) cc_final: 0.3688 (pmt-80) REVERT: C 936 LYS cc_start: 0.8181 (ptmm) cc_final: 0.7846 (mmtp) REVERT: C 979 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8441 (tp) REVERT: C 983 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.6560 (t80) REVERT: C 1142 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6931 (tm-30) REVERT: C 1203 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8051 (tm-30) REVERT: C 1233 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7554 (tpp80) REVERT: D 240 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7108 (t-90) REVERT: D 292 SER cc_start: 0.8729 (t) cc_final: 0.8442 (t) REVERT: D 568 MET cc_start: 0.8760 (tpt) cc_final: 0.8444 (tpt) REVERT: D 687 MET cc_start: 0.6780 (mmt) cc_final: 0.6299 (mmp) REVERT: D 862 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.3668 (pmt-80) REVERT: D 936 LYS cc_start: 0.8103 (ptmm) cc_final: 0.7758 (mmtp) REVERT: D 958 MET cc_start: 0.8410 (tmm) cc_final: 0.8033 (tmm) REVERT: D 983 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.6960 (t80) REVERT: D 1142 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6971 (tm-30) REVERT: D 1203 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7982 (tm-30) outliers start: 109 outliers final: 81 residues processed: 514 average time/residue: 0.2033 time to fit residues: 170.5446 Evaluate side-chains 522 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 424 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1230 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 862 ARG Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 862 ARG Chi-restraints excluded: chain C residue 883 ILE Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1006 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1146 LEU Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 652 LYS Chi-restraints excluded: chain D residue 665 MET Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 862 ARG Chi-restraints excluded: chain D residue 883 ILE Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1150 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 0.0970 chunk 311 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116073 restraints weight = 56216.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120186 restraints weight = 28964.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122973 restraints weight = 19378.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124826 restraints weight = 14997.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.126030 restraints weight = 12607.138| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32968 Z= 0.183 Angle : 0.576 10.003 44584 Z= 0.289 Chirality : 0.040 0.204 4980 Planarity : 0.004 0.077 5516 Dihedral : 7.722 59.709 4551 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.20 % Allowed : 17.15 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3824 helix: 1.58 (0.11), residues: 2412 sheet: -1.93 (0.34), residues: 236 loop : -1.46 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1206 TYR 0.021 0.001 TYR A 479 PHE 0.021 0.001 PHE A1059 TRP 0.016 0.001 TRP A 763 HIS 0.009 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (32968) covalent geometry : angle 0.57583 / 0.29 (44584) hydrogen bonds : bond 0.04912 / 3.33 ( 1683) hydrogen bonds : angle 3.69625 / 2.63 ( 5001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 429 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7514 (t-90) REVERT: A 354 ARG cc_start: 0.8941 (mtp-110) cc_final: 0.8372 (ttm110) REVERT: A 568 MET cc_start: 0.9070 (tpt) cc_final: 0.8691 (tpt) REVERT: A 584 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8411 (tt) REVERT: A 763 TRP cc_start: 0.9172 (OUTLIER) cc_final: 0.8627 (t-100) REVERT: A 862 ARG cc_start: 0.5426 (OUTLIER) cc_final: 0.3371 (pmt-80) REVERT: A 936 LYS cc_start: 0.8177 (ptmm) cc_final: 0.7763 (mmtp) REVERT: A 979 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8438 (tp) REVERT: A 983 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.6611 (t80) REVERT: A 1022 MET cc_start: 0.7477 (mmt) cc_final: 0.7230 (mmt) REVERT: A 1142 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7182 (tm-30) REVERT: A 1158 MET cc_start: 0.6238 (tpp) cc_final: 0.5844 (tmm) REVERT: A 1203 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8068 (tm-30) REVERT: A 1233 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7482 (tpp80) REVERT: B 240 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7142 (t70) REVERT: B 352 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8361 (m-10) REVERT: B 354 ARG cc_start: 0.8884 (mtp-110) cc_final: 0.8179 (ttm110) REVERT: B 568 MET cc_start: 0.9066 (tpt) cc_final: 0.8680 (tpt) REVERT: B 763 TRP cc_start: 0.9186 (OUTLIER) cc_final: 0.8716 (t-100) REVERT: B 862 ARG cc_start: 0.5455 (OUTLIER) cc_final: 0.3403 (pmt-80) REVERT: B 936 LYS cc_start: 0.8201 (ptmm) cc_final: 0.7866 (mmtp) REVERT: B 983 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7083 (t80) REVERT: B 1002 MET cc_start: 0.7856 (mmm) cc_final: 0.7495 (mtt) REVERT: B 1010 MET cc_start: 0.7711 (ttp) cc_final: 0.7388 (ttm) REVERT: B 1022 MET cc_start: 0.7450 (mmt) cc_final: 0.7201 (mmt) REVERT: B 1142 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7136 (tm-30) REVERT: B 1158 MET cc_start: 0.6253 (tpp) cc_final: 0.5854 (tmm) REVERT: B 1203 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8053 (tm-30) REVERT: C 235 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: C 238 LYS cc_start: 0.8401 (mmtp) cc_final: 0.8096 (mmmm) REVERT: C 354 ARG cc_start: 0.8920 (mtp-110) cc_final: 0.8321 (ttm110) REVERT: C 568 MET cc_start: 0.9046 (tpt) cc_final: 0.8659 (tpt) REVERT: C 687 MET cc_start: 0.6859 (mmt) cc_final: 0.6344 (mmp) REVERT: C 862 ARG cc_start: 0.5478 (OUTLIER) cc_final: 0.3407 (pmt-80) REVERT: C 936 LYS cc_start: 0.8204 (ptmm) cc_final: 0.7768 (mmtp) REVERT: C 979 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8424 (tp) REVERT: C 983 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.6620 (t80) REVERT: C 1142 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7071 (tm-30) REVERT: C 1203 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8037 (tm-30) REVERT: C 1233 ARG cc_start: 0.8080 (tpp80) cc_final: 0.7431 (tpp80) REVERT: D 240 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7123 (t-90) REVERT: D 292 SER cc_start: 0.8772 (t) cc_final: 0.8421 (t) REVERT: D 568 MET cc_start: 0.9054 (tpt) cc_final: 0.8669 (tpt) REVERT: D 687 MET cc_start: 0.6795 (mmt) cc_final: 0.6265 (mmp) REVERT: D 862 ARG cc_start: 0.5435 (OUTLIER) cc_final: 0.3383 (pmt-80) REVERT: D 936 LYS cc_start: 0.8210 (ptmm) cc_final: 0.7782 (mmtp) REVERT: D 958 MET cc_start: 0.8455 (tmm) cc_final: 0.8182 (ttp) REVERT: D 983 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7106 (t80) REVERT: D 1049 MET cc_start: 0.7697 (tpt) cc_final: 0.7482 (tpt) REVERT: D 1062 GLN cc_start: 0.8157 (tt0) cc_final: 0.7882 (tt0) REVERT: D 1142 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7154 (tm-30) REVERT: D 1203 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8030 (tm-30) outliers start: 110 outliers final: 85 residues processed: 506 average time/residue: 0.2086 time to fit residues: 172.9845 Evaluate side-chains 524 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 421 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 763 TRP Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 862 ARG Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 652 LYS Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 862 ARG Chi-restraints excluded: chain C residue 883 ILE Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1006 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1146 LEU Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 652 LYS Chi-restraints excluded: chain D residue 665 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 862 ARG Chi-restraints excluded: chain D residue 883 ILE Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1150 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 105 optimal weight: 6.9990 chunk 259 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 249 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 289 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 234 optimal weight: 0.9980 chunk 253 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 354 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1115 ASN B1116 ASN C1115 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121299 restraints weight = 53620.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125491 restraints weight = 27224.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128202 restraints weight = 18043.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130051 restraints weight = 13918.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131239 restraints weight = 11696.366| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 32968 Z= 0.115 Angle : 0.533 10.622 44584 Z= 0.267 Chirality : 0.038 0.159 4980 Planarity : 0.004 0.077 5516 Dihedral : 7.491 59.140 4551 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.77 % Allowed : 17.47 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.15), residues: 3824 helix: 1.77 (0.11), residues: 2416 sheet: -1.85 (0.34), residues: 236 loop : -1.49 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1206 TYR 0.019 0.001 TYR A 479 PHE 0.020 0.001 PHE A1059 TRP 0.012 0.001 TRP A 763 HIS 0.008 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (32968) covalent geometry : angle 0.53287 / 0.27 (44584) hydrogen bonds : bond 0.04185 / 2.84 ( 1683) hydrogen bonds : angle 3.45658 / 2.46 ( 5001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 459 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 243 LYS cc_start: 0.8317 (mptt) cc_final: 0.8098 (mptt) REVERT: A 248 ILE cc_start: 0.8977 (mm) cc_final: 0.8729 (mm) REVERT: A 354 ARG cc_start: 0.8804 (mtp-110) cc_final: 0.8322 (ttm110) REVERT: A 568 MET cc_start: 0.8935 (tpt) cc_final: 0.8626 (tpt) REVERT: A 584 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8472 (tt) REVERT: A 862 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.3585 (pmt-80) REVERT: A 936 LYS cc_start: 0.8147 (ptmm) cc_final: 0.7776 (mmtp) REVERT: A 979 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8394 (tp) REVERT: A 983 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.6575 (t80) REVERT: A 1022 MET cc_start: 0.7457 (mmt) cc_final: 0.7227 (mmt) REVERT: A 1158 MET cc_start: 0.6437 (tpp) cc_final: 0.5868 (tmm) REVERT: A 1203 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7985 (tm-30) REVERT: A 1233 ARG cc_start: 0.7989 (tpp80) cc_final: 0.7502 (tpp80) REVERT: B 354 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.8145 (ttm110) REVERT: B 568 MET cc_start: 0.8932 (tpt) cc_final: 0.8627 (tpt) REVERT: B 710 LEU cc_start: 0.8799 (tp) cc_final: 0.8548 (tt) REVERT: B 763 TRP cc_start: 0.9141 (OUTLIER) cc_final: 0.8759 (t-100) REVERT: B 862 ARG cc_start: 0.5691 (OUTLIER) cc_final: 0.3622 (pmt-80) REVERT: B 936 LYS cc_start: 0.8202 (ptmm) cc_final: 0.7895 (mmtp) REVERT: B 983 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.6870 (t80) REVERT: B 1002 MET cc_start: 0.7687 (mmm) cc_final: 0.7194 (mtt) REVERT: B 1010 MET cc_start: 0.7474 (ttp) cc_final: 0.7211 (ttm) REVERT: B 1022 MET cc_start: 0.7409 (mmt) cc_final: 0.7198 (mmt) REVERT: B 1142 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7000 (tm-30) REVERT: B 1158 MET cc_start: 0.6448 (tpp) cc_final: 0.5865 (tmm) REVERT: B 1203 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 235 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: C 238 LYS cc_start: 0.8437 (mmtp) cc_final: 0.8141 (mmmm) REVERT: C 354 ARG cc_start: 0.8764 (mtp-110) cc_final: 0.8244 (ttm110) REVERT: C 568 MET cc_start: 0.8939 (tpt) cc_final: 0.8646 (tpt) REVERT: C 687 MET cc_start: 0.6825 (mmt) cc_final: 0.6255 (mmp) REVERT: C 862 ARG cc_start: 0.5562 (OUTLIER) cc_final: 0.3535 (pmt-80) REVERT: C 936 LYS cc_start: 0.8170 (ptmm) cc_final: 0.7772 (mmtp) REVERT: C 979 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8428 (tp) REVERT: C 983 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.6551 (t80) REVERT: C 1142 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7013 (tm-30) REVERT: C 1158 MET cc_start: 0.5986 (tpp) cc_final: 0.5776 (tmm) REVERT: C 1203 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 1233 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7402 (tpp80) REVERT: D 240 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.7108 (t-90) REVERT: D 292 SER cc_start: 0.8728 (t) cc_final: 0.8412 (t) REVERT: D 568 MET cc_start: 0.8951 (tpt) cc_final: 0.8660 (tpt) REVERT: D 687 MET cc_start: 0.6806 (mmt) cc_final: 0.6226 (mmp) REVERT: D 763 TRP cc_start: 0.9149 (OUTLIER) cc_final: 0.8682 (t-100) REVERT: D 862 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.3589 (pmt-80) REVERT: D 890 ASN cc_start: 0.9368 (OUTLIER) cc_final: 0.9119 (m-40) REVERT: D 936 LYS cc_start: 0.8071 (ptmm) cc_final: 0.7727 (mmtp) REVERT: D 958 MET cc_start: 0.8419 (tmm) cc_final: 0.8059 (tmm) REVERT: D 983 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.6884 (t80) REVERT: D 1142 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7021 (tm-30) REVERT: D 1158 MET cc_start: 0.5992 (tpp) cc_final: 0.5761 (tmm) REVERT: D 1203 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8038 (tm-30) outliers start: 95 outliers final: 56 residues processed: 523 average time/residue: 0.2006 time to fit residues: 171.9953 Evaluate side-chains 513 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 441 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 763 TRP Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 862 ARG Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 862 ARG Chi-restraints excluded: chain C residue 883 ILE Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1006 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 763 TRP Chi-restraints excluded: chain D residue 862 ARG Chi-restraints excluded: chain D residue 883 ILE Chi-restraints excluded: chain D residue 890 ASN Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1150 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 60 optimal weight: 0.3980 chunk 160 optimal weight: 1.9990 chunk 358 optimal weight: 5.9990 chunk 356 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 chunk 368 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 336 optimal weight: 0.0270 overall best weight: 1.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099620 restraints weight = 54993.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103659 restraints weight = 29341.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.106355 restraints weight = 20217.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108129 restraints weight = 16009.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109281 restraints weight = 13765.103| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32968 Z= 0.162 Angle : 0.578 11.808 44584 Z= 0.289 Chirality : 0.040 0.157 4980 Planarity : 0.004 0.075 5516 Dihedral : 7.439 59.597 4543 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.45 % Allowed : 17.65 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3824 helix: 1.71 (0.11), residues: 2416 sheet: -1.88 (0.34), residues: 236 loop : -1.43 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1226 TYR 0.016 0.001 TYR D1048 PHE 0.021 0.001 PHE A1059 TRP 0.016 0.001 TRP C 466 HIS 0.009 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (32968) covalent geometry : angle 0.57831 / 0.29 (44584) hydrogen bonds : bond 0.04683 / 3.17 ( 1683) hydrogen bonds : angle 3.57999 / 2.54 ( 5001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 438 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 243 LYS cc_start: 0.8388 (mptt) cc_final: 0.8170 (mptt) REVERT: A 248 ILE cc_start: 0.9031 (mm) cc_final: 0.8743 (mm) REVERT: A 354 ARG cc_start: 0.9051 (mtp-110) cc_final: 0.8415 (ttm110) REVERT: A 568 MET cc_start: 0.9082 (tpt) cc_final: 0.8687 (tpt) REVERT: A 584 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8327 (tt) REVERT: A 770 ARG cc_start: 0.8115 (mmt90) cc_final: 0.7899 (mmt90) REVERT: A 862 ARG cc_start: 0.5207 (OUTLIER) cc_final: 0.3224 (pmt-80) REVERT: A 936 LYS cc_start: 0.8084 (ptmm) cc_final: 0.7640 (mmtp) REVERT: A 979 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8394 (tp) REVERT: A 983 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.6496 (t80) REVERT: A 1022 MET cc_start: 0.7360 (mmt) cc_final: 0.7096 (mmt) REVERT: A 1142 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 1158 MET cc_start: 0.6349 (tpp) cc_final: 0.5684 (tmm) REVERT: A 1203 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 1228 GLU cc_start: 0.8608 (tp30) cc_final: 0.8386 (tp30) REVERT: A 1233 ARG cc_start: 0.7974 (tpp80) cc_final: 0.7463 (tpp80) REVERT: B 354 ARG cc_start: 0.9003 (mtp-110) cc_final: 0.8398 (ttm110) REVERT: B 568 MET cc_start: 0.9049 (tpt) cc_final: 0.8660 (tpt) REVERT: B 763 TRP cc_start: 0.9141 (OUTLIER) cc_final: 0.8606 (t-100) REVERT: B 862 ARG cc_start: 0.5259 (OUTLIER) cc_final: 0.3249 (pmt-80) REVERT: B 936 LYS cc_start: 0.8141 (ptmm) cc_final: 0.7768 (mmtp) REVERT: B 983 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7021 (t80) REVERT: B 1002 MET cc_start: 0.7894 (mmm) cc_final: 0.7529 (mtt) REVERT: B 1010 MET cc_start: 0.7654 (ttp) cc_final: 0.7334 (ttm) REVERT: B 1022 MET cc_start: 0.7404 (mmt) cc_final: 0.7182 (mmt) REVERT: B 1142 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7162 (tm-30) REVERT: B 1158 MET cc_start: 0.6313 (tpp) cc_final: 0.5668 (tmm) REVERT: B 1203 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7930 (tm-30) REVERT: C 235 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: C 238 LYS cc_start: 0.8360 (mmtp) cc_final: 0.8056 (mmmm) REVERT: C 354 ARG cc_start: 0.9001 (mtp-110) cc_final: 0.8339 (ttm110) REVERT: C 568 MET cc_start: 0.9052 (tpt) cc_final: 0.8656 (tpt) REVERT: C 687 MET cc_start: 0.6811 (mmt) cc_final: 0.6226 (mmp) REVERT: C 862 ARG cc_start: 0.5290 (OUTLIER) cc_final: 0.3272 (pmt-80) REVERT: C 936 LYS cc_start: 0.8121 (ptmm) cc_final: 0.7704 (mmtp) REVERT: C 979 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8388 (tp) REVERT: C 983 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.6491 (t80) REVERT: C 1142 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7110 (tm-30) REVERT: C 1203 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8022 (tm-30) REVERT: C 1233 ARG cc_start: 0.7896 (tpp80) cc_final: 0.7298 (tpp80) REVERT: D 240 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7099 (t-90) REVERT: D 292 SER cc_start: 0.8731 (t) cc_final: 0.8374 (t) REVERT: D 568 MET cc_start: 0.9072 (tpt) cc_final: 0.8680 (tpt) REVERT: D 687 MET cc_start: 0.6811 (mmt) cc_final: 0.6177 (mmp) REVERT: D 763 TRP cc_start: 0.9148 (OUTLIER) cc_final: 0.8612 (t-100) REVERT: D 862 ARG cc_start: 0.5214 (OUTLIER) cc_final: 0.3218 (pmt-80) REVERT: D 936 LYS cc_start: 0.8111 (ptmm) cc_final: 0.7680 (mmtp) REVERT: D 958 MET cc_start: 0.8418 (tmm) cc_final: 0.8093 (tmm) REVERT: D 983 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.6973 (t80) REVERT: D 1158 MET cc_start: 0.5878 (tpp) cc_final: 0.5514 (tmm) REVERT: D 1203 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8086 (tm-30) outliers start: 84 outliers final: 63 residues processed: 494 average time/residue: 0.1955 time to fit residues: 158.0010 Evaluate side-chains 507 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 429 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 763 TRP Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 862 ARG Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 862 ARG Chi-restraints excluded: chain C residue 883 ILE Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1006 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 763 TRP Chi-restraints excluded: chain D residue 862 ARG Chi-restraints excluded: chain D residue 883 ILE Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1150 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 49 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1229 ASN D 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101555 restraints weight = 54447.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105686 restraints weight = 28866.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108396 restraints weight = 19764.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110219 restraints weight = 15617.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.111389 restraints weight = 13387.515| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32968 Z= 0.121 Angle : 0.548 11.622 44584 Z= 0.273 Chirality : 0.038 0.140 4980 Planarity : 0.004 0.075 5516 Dihedral : 7.322 59.251 4543 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.42 % Allowed : 17.79 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.15), residues: 3824 helix: 1.80 (0.11), residues: 2416 sheet: -1.78 (0.35), residues: 236 loop : -1.45 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1206 TYR 0.016 0.001 TYR A 981 PHE 0.016 0.001 PHE A1059 TRP 0.024 0.001 TRP A 466 HIS 0.009 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (32968) covalent geometry : angle 0.54759 / 0.27 (44584) hydrogen bonds : bond 0.04204 / 2.85 ( 1683) hydrogen bonds : angle 3.44261 / 2.44 ( 5001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5608.70 seconds wall clock time: 97 minutes 36.87 seconds (5856.87 seconds total)