Starting phenix.real_space_refine on Thu May 29 21:39:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ddr_27339/05_2025/8ddr_27339.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddr_27339/05_2025/8ddr_27339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ddr_27339/05_2025/8ddr_27339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddr_27339/05_2025/8ddr_27339.map" model { file = "/net/cci-nas-00/data/ceres_data/8ddr_27339/05_2025/8ddr_27339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddr_27339/05_2025/8ddr_27339.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 4 5.49 5 S 236 5.16 5 Na 2 4.78 5 C 20836 2.51 5 N 5380 2.21 5 O 5616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 1.58s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32074 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7849 Number of conformers: 2 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 8014 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: 7849 Number of conformers: 2 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 8014 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: 7849 Number of conformers: 2 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 8014 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: 7849 Number of conformers: 2 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 8014 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: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' NA': 2, '3PH': 1, '9Z9': 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'3PH': 1, '9Z9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'3PH': 1, '9Z9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'3PH': 1, '9Z9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AMET A1011 " occ=0.57 ... (14 atoms not shown) pdb=" CE BMET A1011 " occ=0.43 residue: pdb=" N AMET B1011 " occ=0.57 ... (14 atoms not shown) pdb=" CE BMET B1011 " occ=0.43 residue: pdb=" N AMET C1011 " occ=0.57 ... (14 atoms not shown) pdb=" CE BMET C1011 " occ=0.43 residue: pdb=" N AMET D1011 " occ=0.57 ... (14 atoms not shown) pdb=" CE BMET D1011 " occ=0.43 Time building chain proxies: 33.96, per 1000 atoms: 1.06 Number of scatterers: 32074 At special positions: 0 Unit cell: (143.302, 143.302, 158.992, 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 236 16.00 P 4 15.00 Na 2 11.00 O 5616 8.00 N 5380 7.00 C 20836 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: 8.68 Conformation dependent library (CDL) restraints added in 7.7 seconds 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7440 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 8 sheets defined 67.3% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 200 through 216 removed outlier: 3.896A pdb=" N VAL A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.778A pdb=" N HIS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.770A 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 Processing helix chain 'A' and resid 308 through 322 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.722A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.509A pdb=" N LEU A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.906A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.569A pdb=" N VAL A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.527A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 636 through 648 removed outlier: 3.929A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.929A pdb=" N GLN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 685 removed outlier: 3.501A pdb=" N ASN A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 784 through 790 removed outlier: 3.678A pdb=" N LEU A 788 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 789 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 790 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 870 through 895 Processing helix chain 'A' and resid 902 through 922 Processing helix chain 'A' and resid 930 through 939 Processing helix chain 'A' and resid 941 through 962 removed outlier: 3.514A pdb=" N VAL A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 removed outlier: 4.267A pdb=" N ILE A 980 " --> pdb=" O CYS A 976 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR A 981 " --> pdb=" O VAL A 977 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 991 removed outlier: 3.874A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1033 removed outlier: 4.047A pdb=" N TYR A 999 " --> pdb=" O TYR A 995 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP A1009 " --> pdb=" O LYS A1005 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A1013 " --> pdb=" O ASP A1009 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A1015 " --> pdb=" O AMET A1011 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1046 removed outlier: 3.735A pdb=" N ILE A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1053 Processing helix chain 'A' and resid 1054 through 1056 No H-bonds generated for 'chain 'A' and resid 1054 through 1056' Processing helix chain 'A' and resid 1059 through 1064 removed outlier: 3.767A pdb=" N ASP A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1117 removed outlier: 4.118A pdb=" N ALA A1093 " --> pdb=" O TRP A1089 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A1104 " --> pdb=" O LEU A1100 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A1106 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL A1107 " --> pdb=" O ASN A1103 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A1108 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1143 removed outlier: 4.709A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1150 Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 3.826A pdb=" N MET A1158 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A1159 " --> pdb=" O HIS A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1214 Processing helix chain 'A' and resid 1215 through 1240 removed outlier: 3.751A pdb=" N ARG A1240 " --> pdb=" O GLU A1236 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 6 removed outlier: 3.671A pdb=" N UNK E 4 " --> pdb=" O UNK E 1 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N UNK E 5 " --> pdb=" O UNK E 2 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N UNK E 6 " --> pdb=" O UNK E 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1 through 6' Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 201 through 216 removed outlier: 4.037A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.587A pdb=" N HIS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER B 242 " --> pdb=" O LYS B 238 " (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 308 through 322 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.740A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 414 through 423 removed outlier: 4.146A pdb=" N LYS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 453 removed outlier: 3.570A pdb=" N LEU B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.906A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.572A pdb=" N VAL B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 509 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 528 Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.526A pdb=" N GLY B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 Processing helix chain 'B' and resid 636 through 648 removed outlier: 3.930A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.924A pdb=" N GLN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 685 removed outlier: 3.501A pdb=" N ASN B 685 " --> pdb=" O GLU B 681 " (cutoff:3.500A) 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 765 Processing helix chain 'B' and resid 774 through 783 Processing helix chain 'B' and resid 784 through 790 removed outlier: 3.637A pdb=" N LEU B 788 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 789 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 790 " --> pdb=" O ILE B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 869 Processing helix chain 'B' and resid 870 through 895 Processing helix chain 'B' and resid 902 through 922 Processing helix chain 'B' and resid 930 through 939 removed outlier: 3.564A pdb=" N LYS B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 962 Processing helix chain 'B' and resid 964 through 985 removed outlier: 4.266A pdb=" N ILE B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 991 removed outlier: 3.878A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1033 removed outlier: 4.048A pdb=" N TYR B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE B1008 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP B1009 " --> pdb=" O LYS B1005 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B1013 " --> pdb=" O ASP B1009 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B1015 " --> pdb=" O AMET B1011 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1046 removed outlier: 3.730A pdb=" N ILE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1053 Processing helix chain 'B' and resid 1054 through 1056 No H-bonds generated for 'chain 'B' and resid 1054 through 1056' Processing helix chain 'B' and resid 1059 through 1064 removed outlier: 3.769A pdb=" N ASP B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1117 removed outlier: 4.110A pdb=" N ALA B1093 " --> pdb=" O TRP B1089 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B1104 " --> pdb=" O LEU B1100 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B1106 " --> pdb=" O ALA B1102 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL B1107 " --> pdb=" O ASN B1103 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B1108 " --> pdb=" O ILE B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1143 removed outlier: 4.707A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1150 Processing helix chain 'B' and resid 1151 through 1163 removed outlier: 3.887A pdb=" N MET B1158 " --> pdb=" O SER B1154 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B1159 " --> pdb=" O HIS B1155 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 removed outlier: 3.753A pdb=" N ARG B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 6 removed outlier: 3.675A pdb=" N UNK F 4 " --> pdb=" O UNK F 1 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N UNK F 5 " --> pdb=" O UNK F 2 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N UNK F 6 " --> pdb=" O UNK F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1 through 6' Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'C' and resid 200 through 216 removed outlier: 3.970A pdb=" N VAL C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.589A pdb=" N HIS C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.978A 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 308 through 322 Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.719A pdb=" N ILE C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 413 through 423 removed outlier: 4.268A pdb=" N LYS C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 453 removed outlier: 3.587A pdb=" N LEU C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 452 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.907A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 removed outlier: 3.570A pdb=" N VAL C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.527A pdb=" N GLY C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 587 Processing helix chain 'C' and resid 636 through 648 removed outlier: 3.928A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.930A pdb=" N GLN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 removed outlier: 3.501A pdb=" N ASN C 685 " --> pdb=" O GLU C 681 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 774 through 783 Processing helix chain 'C' and resid 784 through 790 removed outlier: 3.663A pdb=" N LEU C 788 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 789 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 790 " --> pdb=" O ILE C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 869 Processing helix chain 'C' and resid 870 through 895 Processing helix chain 'C' and resid 902 through 922 Processing helix chain 'C' and resid 930 through 939 removed outlier: 3.526A pdb=" N LYS C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 962 Processing helix chain 'C' and resid 964 through 985 removed outlier: 4.265A pdb=" N ILE C 980 " --> pdb=" O CYS C 976 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR C 981 " --> pdb=" O VAL C 977 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 991 removed outlier: 3.878A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1033 removed outlier: 4.048A pdb=" N TYR C 999 " --> pdb=" O TYR C 995 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C1000 " --> pdb=" O LEU C 996 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP C1009 " --> pdb=" O LYS C1005 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C1013 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C1015 " --> pdb=" O AMET C1011 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1046 removed outlier: 3.735A pdb=" N ILE C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1053 Processing helix chain 'C' and resid 1054 through 1056 No H-bonds generated for 'chain 'C' and resid 1054 through 1056' Processing helix chain 'C' and resid 1059 through 1064 removed outlier: 3.767A pdb=" N ASP C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1117 removed outlier: 4.118A pdb=" N ALA C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C1106 " --> pdb=" O ALA C1102 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL C1107 " --> pdb=" O ASN C1103 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN C1108 " --> pdb=" O ILE C1104 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1143 removed outlier: 4.709A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1150 Processing helix chain 'C' and resid 1151 through 1163 removed outlier: 3.829A pdb=" N MET C1158 " --> pdb=" O SER C1154 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE C1159 " --> pdb=" O HIS C1155 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1214 Processing helix chain 'C' and resid 1215 through 1240 removed outlier: 3.751A pdb=" N ARG C1240 " --> pdb=" O GLU C1236 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 6 removed outlier: 3.672A pdb=" N UNK G 4 " --> pdb=" O UNK G 1 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N UNK G 5 " --> pdb=" O UNK G 2 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N UNK G 6 " --> pdb=" O UNK G 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1 through 6' Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 201 through 216 removed outlier: 4.084A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 244 removed outlier: 3.677A pdb=" N HIS D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 243 " --> pdb=" O ASP D 239 " (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 308 through 322 Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.711A pdb=" N ILE D 346 " --> pdb=" O GLY D 342 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 398 through 402 Processing helix chain 'D' and resid 413 through 423 removed outlier: 4.862A pdb=" N GLU D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 453 removed outlier: 3.550A pdb=" N LEU D 445 " --> pdb=" O ASP D 441 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 468 through 475 removed outlier: 3.906A pdb=" N ALA D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 removed outlier: 3.569A pdb=" N VAL D 497 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 509 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.525A pdb=" N GLY D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 587 Processing helix chain 'D' and resid 636 through 648 removed outlier: 3.927A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 3.930A pdb=" N GLN D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 685 removed outlier: 3.500A pdb=" N ASN D 685 " --> pdb=" O GLU D 681 " (cutoff:3.500A) 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 765 Processing helix chain 'D' and resid 774 through 783 Processing helix chain 'D' and resid 784 through 790 removed outlier: 3.662A pdb=" N LEU D 788 " --> pdb=" O PRO D 785 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 789 " --> pdb=" O SER D 786 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 790 " --> pdb=" O ILE D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 869 Processing helix chain 'D' and resid 870 through 895 Processing helix chain 'D' and resid 902 through 924 removed outlier: 3.542A pdb=" N LEU D 924 " --> pdb=" O MET D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 930 through 939 Processing helix chain 'D' and resid 941 through 962 Processing helix chain 'D' and resid 964 through 985 removed outlier: 4.267A pdb=" N ILE D 980 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 3.872A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1033 removed outlier: 4.048A pdb=" N TYR D 999 " --> pdb=" O TYR D 995 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D1000 " --> pdb=" O LEU D 996 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE D1008 " --> pdb=" O GLY D1004 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D1013 " --> pdb=" O ASP D1009 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D1015 " --> pdb=" O AMET D1011 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE D1016 " --> pdb=" O TYR D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1046 removed outlier: 3.712A pdb=" N ILE D1046 " --> pdb=" O LEU D1042 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1053 Processing helix chain 'D' and resid 1054 through 1056 No H-bonds generated for 'chain 'D' and resid 1054 through 1056' Processing helix chain 'D' and resid 1059 through 1064 removed outlier: 3.768A pdb=" N ASP D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1117 removed outlier: 4.118A pdb=" N ALA D1093 " --> pdb=" O TRP D1089 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU D1106 " --> pdb=" O ALA D1102 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN D1108 " --> pdb=" O ILE D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1118 through 1143 removed outlier: 4.708A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1150 Processing helix chain 'D' and resid 1151 through 1163 removed outlier: 3.826A pdb=" N MET D1158 " --> pdb=" O SER D1154 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE D1159 " --> pdb=" O HIS D1155 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 removed outlier: 3.751A pdb=" N ARG D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 6 removed outlier: 3.673A pdb=" N UNK H 4 " --> pdb=" O UNK H 1 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N UNK H 5 " --> pdb=" O UNK H 2 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N UNK H 6 " --> pdb=" O UNK H 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1 through 6' Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.583A pdb=" N UNK E 10 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 275 removed outlier: 3.550A pdb=" N ALA A 254 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 218 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE A 251 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE A 220 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE A 253 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR A 222 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 185 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 337 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL A 339 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS A 189 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL A 361 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N PHE A 430 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 363 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.578A pdb=" N UNK F 10 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 275 removed outlier: 3.502A pdb=" N VAL B 158 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 254 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 218 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE B 251 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE B 220 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE B 253 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR B 222 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER B 187 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL B 339 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N HIS B 189 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 361 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE B 430 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 363 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.581A pdb=" N UNK G 10 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 271 through 275 removed outlier: 3.500A pdb=" N VAL C 158 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 254 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA C 218 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE C 251 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE C 220 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE C 253 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR C 222 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU C 185 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU C 337 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER C 187 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL C 339 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS C 189 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL C 361 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE C 430 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 363 " --> pdb=" O PHE C 430 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.585A pdb=" N UNK H 10 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 271 through 275 removed outlier: 3.502A pdb=" N VAL D 158 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 254 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA D 218 " --> pdb=" O CYS D 249 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE D 251 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE D 220 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE D 253 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR D 222 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU D 185 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU D 337 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER D 187 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL D 339 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS D 189 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL D 361 " --> pdb=" O THR D 428 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N PHE D 430 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL D 363 " --> pdb=" O PHE D 430 " (cutoff:3.500A) 1764 hydrogen bonds defined for protein. 5254 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: 11.81 Time building geometry restraints manager: 10.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 16 1.04 - 1.26: 5060 1.26 - 1.47: 12834 1.47 - 1.68: 14470 1.68 - 1.90: 436 Bond restraints: 32816 Sorted by residual: bond pdb=" C03 9Z9 A1402 " pdb=" C74 9Z9 A1402 " ideal model delta sigma weight residual 1.534 0.831 0.703 2.00e-02 2.50e+03 1.24e+03 bond pdb=" C03 9Z9 D1401 " pdb=" C74 9Z9 D1401 " ideal model delta sigma weight residual 1.534 0.831 0.703 2.00e-02 2.50e+03 1.24e+03 bond pdb=" C03 9Z9 B1401 " pdb=" C74 9Z9 B1401 " ideal model delta sigma weight residual 1.534 0.831 0.703 2.00e-02 2.50e+03 1.24e+03 bond pdb=" C03 9Z9 C1401 " pdb=" C74 9Z9 C1401 " ideal model delta sigma weight residual 1.534 0.831 0.703 2.00e-02 2.50e+03 1.23e+03 bond pdb=" C02 9Z9 C1401 " pdb=" C03 9Z9 C1401 " ideal model delta sigma weight residual 1.544 1.004 0.540 2.00e-02 2.50e+03 7.30e+02 ... (remaining 32811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.58: 44356 10.58 - 21.15: 4 21.15 - 31.73: 8 31.73 - 42.30: 4 42.30 - 52.88: 4 Bond angle restraints: 44376 Sorted by residual: angle pdb=" C74 9Z9 C1401 " pdb=" C73 9Z9 C1401 " pdb=" C76 9Z9 C1401 " ideal model delta sigma weight residual 114.05 166.93 -52.88 3.00e+00 1.11e-01 3.11e+02 angle pdb=" C74 9Z9 A1402 " pdb=" C73 9Z9 A1402 " pdb=" C76 9Z9 A1402 " ideal model delta sigma weight residual 114.05 166.91 -52.86 3.00e+00 1.11e-01 3.10e+02 angle pdb=" C74 9Z9 B1401 " pdb=" C73 9Z9 B1401 " pdb=" C76 9Z9 B1401 " ideal model delta sigma weight residual 114.05 166.87 -52.82 3.00e+00 1.11e-01 3.10e+02 angle pdb=" C74 9Z9 D1401 " pdb=" C73 9Z9 D1401 " pdb=" C76 9Z9 D1401 " ideal model delta sigma weight residual 114.05 166.86 -52.81 3.00e+00 1.11e-01 3.10e+02 angle pdb=" C76 9Z9 D1401 " pdb=" C73 9Z9 D1401 " pdb=" O72 9Z9 D1401 " ideal model delta sigma weight residual 109.02 71.97 37.05 3.00e+00 1.11e-01 1.53e+02 ... (remaining 44371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.26: 19485 29.26 - 58.51: 467 58.51 - 87.77: 25 87.77 - 117.02: 0 117.02 - 146.28: 4 Dihedral angle restraints: 19981 sinusoidal: 8473 harmonic: 11508 Sorted by residual: dihedral pdb=" C22 9Z9 D1401 " pdb=" C23 9Z9 D1401 " pdb=" C48 9Z9 D1401 " pdb=" O49 9Z9 D1401 " ideal model delta sinusoidal sigma weight residual 177.15 30.87 146.28 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C22 9Z9 C1401 " pdb=" C23 9Z9 C1401 " pdb=" C48 9Z9 C1401 " pdb=" O49 9Z9 C1401 " ideal model delta sinusoidal sigma weight residual 177.15 30.97 146.18 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C22 9Z9 A1402 " pdb=" C23 9Z9 A1402 " pdb=" C48 9Z9 A1402 " pdb=" O49 9Z9 A1402 " ideal model delta sinusoidal sigma weight residual 177.15 31.62 145.53 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 19978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.375: 4940 0.375 - 0.750: 8 0.750 - 1.125: 4 1.125 - 1.501: 0 1.501 - 1.876: 4 Chirality restraints: 4956 Sorted by residual: chirality pdb=" C03 9Z9 C1401 " pdb=" C02 9Z9 C1401 " pdb=" C04 9Z9 C1401 " pdb=" C74 9Z9 C1401 " both_signs ideal model delta sigma weight residual False 2.78 0.91 1.88 2.00e-01 2.50e+01 8.80e+01 chirality pdb=" C03 9Z9 B1401 " pdb=" C02 9Z9 B1401 " pdb=" C04 9Z9 B1401 " pdb=" C74 9Z9 B1401 " both_signs ideal model delta sigma weight residual False 2.78 0.91 1.88 2.00e-01 2.50e+01 8.80e+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 0.91 1.88 2.00e-01 2.50e+01 8.79e+01 ... (remaining 4953 not shown) Planarity restraints: 5516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 784 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO D 785 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 785 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 785 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 784 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 785 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 785 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 785 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 784 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 785 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 785 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 785 " -0.023 5.00e-02 4.00e+02 ... (remaining 5513 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6497 2.78 - 3.31: 31019 3.31 - 3.84: 49986 3.84 - 4.37: 57581 4.37 - 4.90: 102452 Nonbonded interactions: 247535 Sorted by model distance: nonbonded pdb=" C01 9Z9 B1401 " pdb=" C74 9Z9 B1401 " model vdw 2.251 2.944 nonbonded pdb=" C01 9Z9 D1401 " pdb=" C74 9Z9 D1401 " model vdw 2.251 2.944 nonbonded pdb=" C01 9Z9 A1402 " pdb=" C74 9Z9 A1402 " model vdw 2.252 2.944 nonbonded pdb=" C01 9Z9 C1401 " pdb=" C74 9Z9 C1401 " model vdw 2.252 2.944 nonbonded pdb=" OD1 ASN C 194 " pdb=" OH TYR D 479 " model vdw 2.258 3.040 ... (remaining 247530 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 129 through 1010 or resid 1012 through 1243)) selection = (chain 'B' and (resid 129 through 1010 or resid 1012 through 1243)) selection = (chain 'C' and (resid 129 through 1010 or resid 1012 through 1243)) selection = (chain 'D' and (resid 129 through 1010 or resid 1012 through 1243)) } 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.240 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: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 91.750 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.230 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 0.703 32816 Z= 0.741 Angle : 0.936 52.881 44376 Z= 0.359 Chirality : 0.073 1.876 4956 Planarity : 0.003 0.040 5516 Dihedral : 11.799 146.279 12541 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.77 % Allowed : 4.66 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.14), residues: 3836 helix: 1.89 (0.11), residues: 2440 sheet: 1.05 (0.36), residues: 216 loop : -1.35 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 982 HIS 0.002 0.000 HIS C 680 PHE 0.009 0.001 PHE D 376 TYR 0.010 0.001 TYR D1048 ARG 0.003 0.000 ARG C1226 Details of bonding type rmsd hydrogen bonds : bond 0.15863 ( 1764) hydrogen bonds : angle 4.73236 ( 5254) covalent geometry : bond 0.01481 (32816) covalent geometry : angle 0.93626 (44376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 338 time to evaluate : 4.007 Fit side-chains REVERT: A 350 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7426 (mt) REVERT: A 412 HIS cc_start: 0.4523 (OUTLIER) cc_final: 0.3243 (m-70) REVERT: A 930 LYS cc_start: 0.6086 (tmtt) cc_final: 0.5805 (mtpp) REVERT: A 948 LEU cc_start: 0.8481 (tp) cc_final: 0.8266 (tp) REVERT: C 350 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7364 (mt) REVERT: C 412 HIS cc_start: 0.4871 (OUTLIER) cc_final: 0.3841 (m-70) REVERT: C 665 MET cc_start: 0.7804 (ttp) cc_final: 0.7596 (ttp) REVERT: D 350 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7141 (mt) REVERT: D 412 HIS cc_start: 0.5150 (OUTLIER) cc_final: 0.4133 (m-70) REVERT: D 435 GLU cc_start: 0.5093 (OUTLIER) cc_final: 0.4854 (pp20) outliers start: 61 outliers final: 30 residues processed: 389 average time/residue: 0.4107 time to fit residues: 260.8663 Evaluate side-chains 308 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 1217 ASP Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 877 PHE 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 327 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN A 232 HIS A 275 GLN A 314 GLN A 412 HIS A 575 ASN A 719 GLN A 739 GLN A 933 GLN A1115 ASN A1116 ASN A1141 HIS A1199 GLN B 134 GLN B 232 HIS B 275 GLN B 314 GLN B 719 GLN B 739 GLN B 933 GLN B1115 ASN B1116 ASN B1141 HIS B1199 GLN C 134 GLN C 232 HIS C 275 GLN C 314 GLN C 412 HIS C 575 ASN C 719 GLN C 739 GLN C 933 GLN C1115 ASN C1116 ASN C1141 HIS C1199 GLN D 134 GLN ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN D 314 GLN D 575 ASN D 719 GLN D 739 GLN D1115 ASN D1116 ASN D1141 HIS D1199 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.092105 restraints weight = 76160.952| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.99 r_work: 0.2975 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 32816 Z= 0.260 Angle : 0.670 8.637 44376 Z= 0.342 Chirality : 0.045 0.196 4956 Planarity : 0.005 0.041 5516 Dihedral : 10.464 143.123 4871 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.31 % Allowed : 8.00 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3836 helix: 1.42 (0.11), residues: 2452 sheet: 0.34 (0.32), residues: 244 loop : -1.56 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 763 HIS 0.005 0.001 HIS B 680 PHE 0.016 0.002 PHE A1059 TYR 0.020 0.002 TYR D1012 ARG 0.022 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.07424 ( 1764) hydrogen bonds : angle 4.01972 ( 5254) covalent geometry : bond 0.00642 (32816) covalent geometry : angle 0.67019 (44376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 294 time to evaluate : 3.551 Fit side-chains REVERT: A 350 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7800 (mt) REVERT: A 414 PHE cc_start: 0.6062 (m-80) cc_final: 0.5783 (m-80) REVERT: A 418 MET cc_start: 0.6280 (mmt) cc_final: 0.5921 (mmt) REVERT: A 913 PHE cc_start: 0.8275 (t80) cc_final: 0.7993 (t80) REVERT: B 350 LEU cc_start: 0.8196 (mt) cc_final: 0.7840 (mt) REVERT: B 421 MET cc_start: 0.6720 (mmm) cc_final: 0.6417 (mmt) REVERT: B 769 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7083 (ptt) REVERT: B 913 PHE cc_start: 0.8268 (t80) cc_final: 0.7993 (t80) REVERT: C 350 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7605 (mt) REVERT: C 414 PHE cc_start: 0.5832 (m-80) cc_final: 0.5614 (m-80) REVERT: C 442 LEU cc_start: 0.8815 (mt) cc_final: 0.8589 (mp) REVERT: C 913 PHE cc_start: 0.8248 (t80) cc_final: 0.7963 (t80) REVERT: D 412 HIS cc_start: 0.4399 (OUTLIER) cc_final: 0.3890 (m-70) REVERT: D 479 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.5647 (m-80) REVERT: D 913 PHE cc_start: 0.8259 (t80) cc_final: 0.7979 (t80) REVERT: D 936 LYS cc_start: 0.7232 (mttm) cc_final: 0.6754 (mmmm) outliers start: 45 outliers final: 36 residues processed: 330 average time/residue: 0.3961 time to fit residues: 215.4278 Evaluate side-chains 321 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 1158 MET Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 1158 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 746 HIS Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 1158 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 321 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 207 optimal weight: 0.1980 chunk 257 optimal weight: 0.7980 chunk 325 optimal weight: 3.9990 chunk 315 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A1238 ASN C1238 ASN D 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095919 restraints weight = 81503.224| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.18 r_work: 0.3018 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32816 Z= 0.120 Angle : 0.520 7.759 44376 Z= 0.265 Chirality : 0.038 0.143 4956 Planarity : 0.004 0.037 5516 Dihedral : 9.953 135.455 4853 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.04 % Allowed : 7.74 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3836 helix: 1.69 (0.11), residues: 2492 sheet: 0.63 (0.35), residues: 224 loop : -1.40 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 763 HIS 0.004 0.001 HIS A 378 PHE 0.020 0.001 PHE D 376 TYR 0.012 0.001 TYR C 878 ARG 0.009 0.000 ARG A 768 Details of bonding type rmsd hydrogen bonds : bond 0.05389 ( 1764) hydrogen bonds : angle 3.60113 ( 5254) covalent geometry : bond 0.00254 (32816) covalent geometry : angle 0.51963 (44376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 292 time to evaluate : 3.824 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7596 (mt) REVERT: A 418 MET cc_start: 0.6501 (mmt) cc_final: 0.6209 (mmt) REVERT: A 930 LYS cc_start: 0.6400 (tmtt) cc_final: 0.5829 (mtpp) REVERT: A 983 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.7410 (t80) REVERT: B 350 LEU cc_start: 0.8177 (mt) cc_final: 0.7735 (mt) REVERT: B 354 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7680 (mtm-85) REVERT: B 421 MET cc_start: 0.6683 (mmm) cc_final: 0.6457 (mmt) REVERT: B 769 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6882 (ptt) REVERT: B 983 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.7418 (t80) REVERT: C 350 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7630 (mt) REVERT: C 983 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.7410 (t80) REVERT: D 412 HIS cc_start: 0.4316 (OUTLIER) cc_final: 0.3731 (m-70) REVERT: D 479 TYR cc_start: 0.5779 (OUTLIER) cc_final: 0.5243 (m-80) REVERT: D 936 LYS cc_start: 0.7169 (mttm) cc_final: 0.6800 (mmmm) REVERT: D 983 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.7405 (t80) outliers start: 70 outliers final: 35 residues processed: 349 average time/residue: 0.4026 time to fit residues: 234.5141 Evaluate side-chains 328 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 746 HIS Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 983 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 44 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 378 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 373 optimal weight: 0.8980 chunk 299 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 336 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A1238 ASN C 575 ASN C1238 ASN D 575 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.092771 restraints weight = 97519.315| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.46 r_work: 0.2925 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 32816 Z= 0.215 Angle : 0.608 9.218 44376 Z= 0.309 Chirality : 0.042 0.155 4956 Planarity : 0.005 0.041 5516 Dihedral : 9.851 128.423 4853 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.07 % Allowed : 8.35 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3836 helix: 1.56 (0.11), residues: 2460 sheet: 0.33 (0.34), residues: 224 loop : -1.49 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 763 HIS 0.005 0.001 HIS D 680 PHE 0.028 0.002 PHE A 162 TYR 0.014 0.002 TYR D1012 ARG 0.006 0.001 ARG D 768 Details of bonding type rmsd hydrogen bonds : bond 0.06905 ( 1764) hydrogen bonds : angle 3.78520 ( 5254) covalent geometry : bond 0.00527 (32816) covalent geometry : angle 0.60753 (44376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 272 time to evaluate : 4.062 Fit side-chains REVERT: A 173 MET cc_start: 0.8497 (mtp) cc_final: 0.8284 (mtp) REVERT: A 350 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7751 (mt) REVERT: A 418 MET cc_start: 0.6216 (mmt) cc_final: 0.5822 (mmt) REVERT: A 421 MET cc_start: 0.8039 (mmp) cc_final: 0.7763 (mmp) REVERT: B 173 MET cc_start: 0.8515 (mtp) cc_final: 0.8313 (mtp) REVERT: B 350 LEU cc_start: 0.8151 (mt) cc_final: 0.7698 (mt) REVERT: B 421 MET cc_start: 0.6760 (mmm) cc_final: 0.6544 (mmt) REVERT: B 769 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6912 (ptt) REVERT: C 350 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7477 (mt) REVERT: C 412 HIS cc_start: 0.4326 (OUTLIER) cc_final: 0.3760 (m170) REVERT: D 412 HIS cc_start: 0.4489 (OUTLIER) cc_final: 0.3873 (m-70) REVERT: D 479 TYR cc_start: 0.5881 (OUTLIER) cc_final: 0.5382 (m-80) REVERT: D 936 LYS cc_start: 0.7136 (mttm) cc_final: 0.6708 (mmmm) outliers start: 71 outliers final: 43 residues processed: 326 average time/residue: 0.3875 time to fit residues: 212.0059 Evaluate side-chains 320 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 575 ASN Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 746 HIS Chi-restraints excluded: chain D residue 1022 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 89 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 174 optimal weight: 0.5980 chunk 339 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 3 optimal weight: 0.0060 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN C 575 ASN D 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.091621 restraints weight = 84230.595| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.53 r_work: 0.2996 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 32816 Z= 0.124 Angle : 0.523 9.822 44376 Z= 0.266 Chirality : 0.039 0.142 4956 Planarity : 0.004 0.039 5516 Dihedral : 9.580 120.176 4847 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.12 % Allowed : 8.47 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3836 helix: 1.78 (0.11), residues: 2468 sheet: 0.51 (0.35), residues: 224 loop : -1.42 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 763 HIS 0.002 0.001 HIS A 680 PHE 0.026 0.001 PHE A 162 TYR 0.009 0.001 TYR C 878 ARG 0.006 0.000 ARG B 768 Details of bonding type rmsd hydrogen bonds : bond 0.05589 ( 1764) hydrogen bonds : angle 3.56420 ( 5254) covalent geometry : bond 0.00269 (32816) covalent geometry : angle 0.52295 (44376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 272 time to evaluate : 3.586 Fit side-chains REVERT: A 173 MET cc_start: 0.8461 (mtp) cc_final: 0.8166 (mtp) REVERT: A 350 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7775 (mt) REVERT: A 418 MET cc_start: 0.6437 (mmt) cc_final: 0.6103 (mmt) REVERT: A 421 MET cc_start: 0.7958 (mmp) cc_final: 0.7734 (mmp) REVERT: A 930 LYS cc_start: 0.6376 (tmtt) cc_final: 0.5840 (mtpp) REVERT: A 983 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.7377 (t80) REVERT: B 173 MET cc_start: 0.8471 (mtp) cc_final: 0.8182 (mtp) REVERT: B 350 LEU cc_start: 0.8197 (mt) cc_final: 0.7737 (mt) REVERT: B 769 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6862 (ptt) REVERT: B 983 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.7383 (t80) REVERT: C 350 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7613 (mt) REVERT: C 983 TYR cc_start: 0.9225 (OUTLIER) cc_final: 0.7380 (t80) REVERT: D 412 HIS cc_start: 0.4333 (OUTLIER) cc_final: 0.3687 (m-70) REVERT: D 414 PHE cc_start: 0.6340 (m-80) cc_final: 0.6124 (m-80) REVERT: D 479 TYR cc_start: 0.5688 (OUTLIER) cc_final: 0.5261 (m-80) REVERT: D 936 LYS cc_start: 0.7048 (mttm) cc_final: 0.6655 (mmmm) REVERT: D 983 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.7374 (t80) outliers start: 73 outliers final: 54 residues processed: 330 average time/residue: 0.3934 time to fit residues: 219.1332 Evaluate side-chains 328 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1158 MET Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1158 MET Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1158 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 746 HIS Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1150 LEU Chi-restraints excluded: chain D residue 1158 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 0.7980 chunk 262 optimal weight: 3.9990 chunk 201 optimal weight: 0.2980 chunk 381 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN C 575 ASN D 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.127378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096649 restraints weight = 93221.624| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.36 r_work: 0.2987 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32816 Z= 0.121 Angle : 0.511 10.630 44376 Z= 0.259 Chirality : 0.038 0.137 4956 Planarity : 0.004 0.040 5516 Dihedral : 9.276 104.677 4847 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.18 % Allowed : 8.70 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.14), residues: 3836 helix: 1.92 (0.11), residues: 2464 sheet: 0.59 (0.35), residues: 224 loop : -1.36 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 763 HIS 0.002 0.001 HIS B1141 PHE 0.025 0.001 PHE A 162 TYR 0.009 0.001 TYR C 878 ARG 0.006 0.000 ARG D 768 Details of bonding type rmsd hydrogen bonds : bond 0.05197 ( 1764) hydrogen bonds : angle 3.44054 ( 5254) covalent geometry : bond 0.00267 (32816) covalent geometry : angle 0.51095 (44376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 273 time to evaluate : 4.055 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.8419 (mtp) cc_final: 0.8187 (mtp) REVERT: A 350 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7382 (mt) REVERT: A 354 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7294 (mtt180) REVERT: A 418 MET cc_start: 0.6257 (mmt) cc_final: 0.5928 (mmt) REVERT: A 930 LYS cc_start: 0.6363 (tmtt) cc_final: 0.5856 (mtpp) REVERT: A 983 TYR cc_start: 0.9160 (OUTLIER) cc_final: 0.7361 (t80) REVERT: B 173 MET cc_start: 0.8414 (mtp) cc_final: 0.8201 (mtp) REVERT: B 350 LEU cc_start: 0.8164 (mt) cc_final: 0.7661 (mt) REVERT: B 769 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6708 (ptt) REVERT: B 925 MET cc_start: 0.7316 (mmt) cc_final: 0.6515 (tmm) REVERT: B 983 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.7359 (t80) REVERT: C 350 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7595 (mt) REVERT: C 412 HIS cc_start: 0.4209 (OUTLIER) cc_final: 0.3583 (m170) REVERT: C 983 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.7361 (t80) REVERT: D 412 HIS cc_start: 0.4551 (OUTLIER) cc_final: 0.3693 (m-70) REVERT: D 479 TYR cc_start: 0.5867 (OUTLIER) cc_final: 0.5333 (m-80) REVERT: D 936 LYS cc_start: 0.6944 (mttm) cc_final: 0.6631 (mmmm) REVERT: D 983 TYR cc_start: 0.9156 (OUTLIER) cc_final: 0.7353 (t80) outliers start: 75 outliers final: 53 residues processed: 335 average time/residue: 0.4070 time to fit residues: 226.9106 Evaluate side-chains 330 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 266 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 575 ASN Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 SER Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 746 HIS Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1022 MET 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 233 optimal weight: 3.9990 chunk 309 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 294 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 202 optimal weight: 0.6980 chunk 351 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN C 575 ASN D 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096785 restraints weight = 106870.974| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.52 r_work: 0.2976 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 32816 Z= 0.117 Angle : 0.512 8.889 44376 Z= 0.257 Chirality : 0.038 0.137 4956 Planarity : 0.004 0.040 5516 Dihedral : 9.147 98.335 4847 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.98 % Allowed : 9.02 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.14), residues: 3836 helix: 1.99 (0.11), residues: 2464 sheet: 0.64 (0.35), residues: 224 loop : -1.34 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 763 HIS 0.002 0.000 HIS A 680 PHE 0.023 0.001 PHE A 162 TYR 0.009 0.001 TYR C 576 ARG 0.005 0.000 ARG B 768 Details of bonding type rmsd hydrogen bonds : bond 0.05072 ( 1764) hydrogen bonds : angle 3.40933 ( 5254) covalent geometry : bond 0.00255 (32816) covalent geometry : angle 0.51188 (44376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 271 time to evaluate : 3.683 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7406 (mt) REVERT: A 354 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7274 (mtt180) REVERT: A 418 MET cc_start: 0.6261 (mmt) cc_final: 0.5998 (mmt) REVERT: A 930 LYS cc_start: 0.6362 (tmtt) cc_final: 0.5853 (mtpp) REVERT: A 983 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.7327 (t80) REVERT: B 173 MET cc_start: 0.8412 (mtp) cc_final: 0.8195 (mtp) REVERT: B 354 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7419 (mtp180) REVERT: B 769 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.6701 (ptt) REVERT: B 983 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.7344 (t80) REVERT: C 350 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7573 (mt) REVERT: C 412 HIS cc_start: 0.4104 (OUTLIER) cc_final: 0.3505 (m170) REVERT: C 983 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.7342 (t80) REVERT: D 412 HIS cc_start: 0.4482 (OUTLIER) cc_final: 0.3657 (m-70) REVERT: D 479 TYR cc_start: 0.5696 (OUTLIER) cc_final: 0.5249 (m-80) REVERT: D 936 LYS cc_start: 0.6955 (mttm) cc_final: 0.6624 (mmmm) REVERT: D 983 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.7321 (t80) outliers start: 68 outliers final: 49 residues processed: 329 average time/residue: 0.3967 time to fit residues: 216.2119 Evaluate side-chains 324 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 746 HIS Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 983 TYR 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 165 optimal weight: 0.0980 chunk 332 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 305 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN C 575 ASN D 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.125891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094242 restraints weight = 89965.697| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.25 r_work: 0.2972 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32816 Z= 0.160 Angle : 0.555 9.145 44376 Z= 0.280 Chirality : 0.040 0.144 4956 Planarity : 0.004 0.040 5516 Dihedral : 9.042 92.886 4847 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.15 % Allowed : 9.16 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.14), residues: 3836 helix: 1.85 (0.11), residues: 2464 sheet: 0.49 (0.35), residues: 224 loop : -1.38 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 763 HIS 0.003 0.001 HIS D 680 PHE 0.023 0.001 PHE A 162 TYR 0.011 0.001 TYR D 585 ARG 0.004 0.000 ARG A 768 Details of bonding type rmsd hydrogen bonds : bond 0.05948 ( 1764) hydrogen bonds : angle 3.53571 ( 5254) covalent geometry : bond 0.00380 (32816) covalent geometry : angle 0.55505 (44376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 264 time to evaluate : 3.910 Fit side-chains REVERT: A 350 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7534 (mt) REVERT: A 354 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7355 (mtt180) REVERT: A 412 HIS cc_start: 0.4056 (OUTLIER) cc_final: 0.3138 (m170) REVERT: A 418 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.6133 (mmm) REVERT: B 350 LEU cc_start: 0.8182 (mt) cc_final: 0.7767 (mt) REVERT: B 769 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.6889 (ptt) REVERT: C 350 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7733 (mt) REVERT: C 412 HIS cc_start: 0.4152 (OUTLIER) cc_final: 0.3523 (m170) REVERT: D 412 HIS cc_start: 0.4315 (OUTLIER) cc_final: 0.3457 (m-70) REVERT: D 479 TYR cc_start: 0.5935 (OUTLIER) cc_final: 0.5467 (m-80) REVERT: D 936 LYS cc_start: 0.7079 (mttm) cc_final: 0.6737 (mmmm) outliers start: 74 outliers final: 55 residues processed: 326 average time/residue: 0.3918 time to fit residues: 213.8831 Evaluate side-chains 325 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 575 ASN Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 746 HIS Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 1022 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 49 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 385 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 296 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN C 575 ASN D 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095075 restraints weight = 102376.110| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.52 r_work: 0.2953 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32816 Z= 0.140 Angle : 0.541 9.586 44376 Z= 0.273 Chirality : 0.039 0.141 4956 Planarity : 0.004 0.041 5516 Dihedral : 8.955 89.212 4847 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.98 % Allowed : 9.40 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.14), residues: 3836 helix: 1.91 (0.11), residues: 2464 sheet: 0.54 (0.35), residues: 224 loop : -1.37 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 763 HIS 0.003 0.000 HIS B 680 PHE 0.024 0.001 PHE C 162 TYR 0.010 0.001 TYR C 585 ARG 0.004 0.000 ARG A 768 Details of bonding type rmsd hydrogen bonds : bond 0.05632 ( 1764) hydrogen bonds : angle 3.49016 ( 5254) covalent geometry : bond 0.00323 (32816) covalent geometry : angle 0.54102 (44376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 265 time to evaluate : 3.848 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7522 (mt) REVERT: A 412 HIS cc_start: 0.4068 (OUTLIER) cc_final: 0.3124 (m170) REVERT: B 350 LEU cc_start: 0.8142 (mt) cc_final: 0.7679 (mt) REVERT: B 769 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.6789 (ptt) REVERT: C 350 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7599 (mt) REVERT: C 412 HIS cc_start: 0.4197 (OUTLIER) cc_final: 0.3547 (m170) REVERT: D 412 HIS cc_start: 0.4473 (OUTLIER) cc_final: 0.3586 (m-70) REVERT: D 479 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.5405 (m-80) REVERT: D 936 LYS cc_start: 0.6968 (mttm) cc_final: 0.6626 (mmmm) outliers start: 68 outliers final: 53 residues processed: 322 average time/residue: 0.4049 time to fit residues: 217.7944 Evaluate side-chains 319 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 259 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 746 HIS Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 1022 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 303 optimal weight: 0.6980 chunk 252 optimal weight: 0.0470 chunk 129 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 200 optimal weight: 0.0770 chunk 242 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 378 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 275 optimal weight: 0.0270 chunk 92 optimal weight: 2.9990 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094426 restraints weight = 85668.833| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.60 r_work: 0.3037 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32816 Z= 0.102 Angle : 0.510 10.647 44376 Z= 0.254 Chirality : 0.038 0.135 4956 Planarity : 0.004 0.041 5516 Dihedral : 8.568 75.926 4847 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.60 % Allowed : 9.78 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.14), residues: 3836 helix: 2.15 (0.11), residues: 2456 sheet: 0.95 (0.36), residues: 220 loop : -1.34 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 763 HIS 0.002 0.000 HIS D 746 PHE 0.021 0.001 PHE B 162 TYR 0.011 0.001 TYR B 352 ARG 0.006 0.000 ARG B 354 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 1764) hydrogen bonds : angle 3.27155 ( 5254) covalent geometry : bond 0.00207 (32816) covalent geometry : angle 0.51034 (44376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 271 time to evaluate : 3.770 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7522 (mt) REVERT: A 930 LYS cc_start: 0.6320 (tmtt) cc_final: 0.5807 (mtpp) REVERT: B 350 LEU cc_start: 0.8032 (mt) cc_final: 0.7535 (mt) REVERT: B 769 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6731 (ptt) REVERT: B 925 MET cc_start: 0.7495 (mmt) cc_final: 0.6509 (tmm) REVERT: C 350 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7592 (mt) REVERT: C 412 HIS cc_start: 0.3698 (OUTLIER) cc_final: 0.3136 (m170) REVERT: D 479 TYR cc_start: 0.5703 (OUTLIER) cc_final: 0.5234 (m-80) REVERT: D 936 LYS cc_start: 0.6915 (mttm) cc_final: 0.6615 (mmmm) outliers start: 55 outliers final: 44 residues processed: 319 average time/residue: 0.4144 time to fit residues: 219.6092 Evaluate side-chains 307 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 633 HIS Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 746 HIS Chi-restraints excluded: chain D residue 877 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 7 optimal weight: 0.5980 chunk 326 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 254 optimal weight: 0.5980 chunk 367 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 369 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN C 575 ASN D 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097535 restraints weight = 101820.552| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.45 r_work: 0.2993 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32816 Z= 0.118 Angle : 0.522 11.100 44376 Z= 0.260 Chirality : 0.038 0.134 4956 Planarity : 0.004 0.041 5516 Dihedral : 8.527 72.158 4845 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.66 % Allowed : 9.63 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.14), residues: 3836 helix: 2.10 (0.11), residues: 2464 sheet: 0.76 (0.36), residues: 224 loop : -1.33 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 763 HIS 0.002 0.000 HIS A 680 PHE 0.021 0.001 PHE A 162 TYR 0.009 0.001 TYR A1051 ARG 0.004 0.000 ARG A 768 Details of bonding type rmsd hydrogen bonds : bond 0.04861 ( 1764) hydrogen bonds : angle 3.30835 ( 5254) covalent geometry : bond 0.00265 (32816) covalent geometry : angle 0.52172 (44376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17129.45 seconds wall clock time: 297 minutes 4.98 seconds (17824.98 seconds total)