Starting phenix.real_space_refine on Mon Jul 6 04:39:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ddu_27342/07_2026/8ddu_27342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddu_27342/07_2026/8ddu_27342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ddu_27342/07_2026/8ddu_27342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddu_27342/07_2026/8ddu_27342.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ddu_27342/07_2026/8ddu_27342.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ddu_27342/07_2026/8ddu_27342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ddu_27342/07_2026/8ddu_27342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddu_27342/07_2026/8ddu_27342.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 232 5.16 5 Na 2 4.78 5 C 20916 2.51 5 N 5376 2.21 5 O 5688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32230 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 133 Unusual residues: {' NA': 2, '3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N APHE A 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE A 913 " occ=0.47 residue: pdb=" N AMET A1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET A1011 " occ=0.57 residue: pdb=" N APHE B 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE B 913 " occ=0.47 residue: pdb=" N AMET B1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET B1011 " occ=0.57 residue: pdb=" N APHE C 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE C 913 " occ=0.47 residue: pdb=" N AMET C1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET C1011 " occ=0.57 residue: pdb=" N APHE D 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE D 913 " occ=0.47 residue: pdb=" N AMET D1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET D1011 " occ=0.57 Time building chain proxies: 5.79, per 1000 atoms: 0.18 Number of scatterers: 32230 At special positions: 0 Unit cell: (147.96, 147.96, 157.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 232 16.00 P 16 15.00 Na 2 11.00 O 5688 8.00 N 5376 7.00 C 20916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7432 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 8 sheets defined 66.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 165 through 175 Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.508A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.918A pdb=" N HIS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.144A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.797A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.728A pdb=" N LYS A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.541A pdb=" N LYS A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.035A 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: 3.619A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.856A pdb=" N GLN A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 556 through 569 Processing helix chain 'A' and resid 574 through 577 Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.924A pdb=" N ASN A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 648 removed outlier: 4.059A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.924A pdb=" N GLN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 685 Processing helix chain 'A' and resid 689 through 717 removed outlier: 3.851A pdb=" N GLN A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.627A pdb=" N THR A 726 " --> pdb=" O MET A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 removed outlier: 3.589A pdb=" N ILE A 750 " --> pdb=" O HIS A 746 " (cutoff:3.500A) 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: 3.521A pdb=" N LEU A 788 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 789 " --> pdb=" O SER A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 870 through 895 Processing helix chain 'A' and resid 902 through 925 Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.824A pdb=" N LYS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 962 removed outlier: 3.662A pdb=" N VAL A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 Processing helix chain 'A' and resid 985 through 991 removed outlier: 4.129A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1033 removed outlier: 3.575A pdb=" N ILE A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1054 removed outlier: 3.615A pdb=" N ILE A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET A1049 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 3.661A pdb=" N ILE A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1105 removed outlier: 4.230A pdb=" N ALA A1093 " --> pdb=" O TRP A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1118 through 1142 removed outlier: 4.541A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.350A 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 1161 removed outlier: 3.553A pdb=" N MET A1158 " --> pdb=" O SER A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1164 No H-bonds generated for 'chain 'A' and resid 1162 through 1164' Processing helix chain 'A' and resid 1186 through 1214 Processing helix chain 'A' and resid 1215 through 1240 Processing helix chain 'B' and resid 165 through 175 Processing helix chain 'B' and resid 201 through 216 removed outlier: 3.509A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.919A pdb=" N HIS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.622A 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 279 through 283 removed outlier: 4.143A pdb=" N LYS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.796A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.728A pdb=" N LYS B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 439 through 453 removed outlier: 3.540A pdb=" N LYS B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 4.035A 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: 3.620A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.856A pdb=" N GLN B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 528 Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 556 through 569 Processing helix chain 'B' and resid 574 through 577 Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.924A pdb=" N ASN B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 648 removed outlier: 4.059A 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 Processing helix chain 'B' and resid 689 through 717 removed outlier: 3.852A pdb=" N GLN B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 727 removed outlier: 3.627A pdb=" N THR B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.589A pdb=" N ILE B 750 " --> pdb=" O HIS B 746 " (cutoff:3.500A) 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: 3.521A pdb=" N LEU B 788 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 789 " --> pdb=" O SER B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 868 Processing helix chain 'B' and resid 870 through 895 Processing helix chain 'B' and resid 902 through 925 Processing helix chain 'B' and resid 930 through 939 removed outlier: 3.824A pdb=" N LYS B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 962 removed outlier: 3.663A pdb=" N VAL B 945 " --> pdb=" O GLU B 941 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 985 Processing helix chain 'B' and resid 985 through 991 removed outlier: 4.128A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1033 removed outlier: 3.575A pdb=" N ILE B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1054 removed outlier: 3.616A pdb=" N ILE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE B1047 " --> pdb=" O ALA B1043 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET B1049 " --> pdb=" O ASN B1045 " (cutoff:3.500A) Proline residue: B1050 - end of helix removed outlier: 3.660A pdb=" N ILE B1054 " --> pdb=" O PRO B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1105 removed outlier: 4.229A pdb=" N ALA B1093 " --> pdb=" O TRP B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1117 Processing helix chain 'B' and resid 1118 through 1142 removed outlier: 4.541A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.349A 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 1161 removed outlier: 3.553A pdb=" N MET B1158 " --> pdb=" O SER B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1164 No H-bonds generated for 'chain 'B' and resid 1162 through 1164' Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 Processing helix chain 'C' and resid 165 through 175 Processing helix chain 'C' and resid 201 through 216 removed outlier: 3.508A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.918A pdb=" N HIS C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'C' and resid 279 through 283 removed outlier: 4.142A pdb=" N LYS C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.796A pdb=" N ILE C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.728A pdb=" N LYS C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 439 through 453 removed outlier: 3.540A pdb=" N LYS C 450 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 4.036A 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: 3.620A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 removed outlier: 3.856A pdb=" N GLN C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 556 through 569 Processing helix chain 'C' and resid 574 through 577 Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.923A pdb=" N ASN C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 648 removed outlier: 4.059A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.924A pdb=" N GLN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 Processing helix chain 'C' and resid 689 through 717 removed outlier: 3.851A pdb=" N GLN C 693 " --> pdb=" O ASP C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 727 removed outlier: 3.627A pdb=" N THR C 726 " --> pdb=" O MET C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.589A pdb=" N ILE C 750 " --> pdb=" O HIS C 746 " (cutoff:3.500A) 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: 3.521A pdb=" N LEU C 788 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 789 " --> pdb=" O SER C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 868 Processing helix chain 'C' and resid 870 through 895 Processing helix chain 'C' and resid 902 through 925 Processing helix chain 'C' and resid 930 through 939 removed outlier: 3.825A pdb=" N LYS C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 962 removed outlier: 3.662A pdb=" N VAL C 945 " --> pdb=" O GLU C 941 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 962 " --> pdb=" O MET C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 985 Processing helix chain 'C' and resid 985 through 991 removed outlier: 4.128A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1033 removed outlier: 3.575A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1054 removed outlier: 3.617A pdb=" N ILE C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE C1047 " --> pdb=" O ALA C1043 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET C1049 " --> pdb=" O ASN C1045 " (cutoff:3.500A) Proline residue: C1050 - end of helix removed outlier: 3.660A pdb=" N ILE C1054 " --> pdb=" O PRO C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1105 removed outlier: 4.230A pdb=" N ALA C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1117 Processing helix chain 'C' and resid 1118 through 1142 removed outlier: 4.540A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.350A 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 1161 removed outlier: 3.552A pdb=" N MET C1158 " --> pdb=" O SER C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1162 through 1164 No H-bonds generated for 'chain 'C' and resid 1162 through 1164' Processing helix chain 'C' and resid 1186 through 1214 Processing helix chain 'C' and resid 1215 through 1240 Processing helix chain 'D' and resid 165 through 175 Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.508A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.918A pdb=" N HIS D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 279 through 283 removed outlier: 4.144A pdb=" N LYS D 283 " --> pdb=" O PRO D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.797A pdb=" N ILE D 346 " --> pdb=" O GLY D 342 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.729A pdb=" N LYS D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 439 through 453 removed outlier: 3.540A pdb=" N LYS D 450 " --> pdb=" O THR D 446 " (cutoff:3.500A) removed outlier: 4.036A 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: 3.620A pdb=" N ALA D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 removed outlier: 3.857A pdb=" N GLN D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 556 through 569 Processing helix chain 'D' and resid 574 through 577 Processing helix chain 'D' and resid 578 through 587 removed outlier: 3.924A pdb=" N ASN D 587 " --> pdb=" O THR D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 648 removed outlier: 4.059A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 3.924A pdb=" N GLN D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 685 Processing helix chain 'D' and resid 689 through 717 removed outlier: 3.851A pdb=" N GLN D 693 " --> pdb=" O ASP D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 727 removed outlier: 3.627A pdb=" N THR D 726 " --> pdb=" O MET D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.590A pdb=" N ILE D 750 " --> pdb=" O HIS D 746 " (cutoff:3.500A) 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: 3.521A pdb=" N LEU D 788 " --> pdb=" O PRO D 785 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 789 " --> pdb=" O SER D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 868 Processing helix chain 'D' and resid 870 through 895 Processing helix chain 'D' and resid 902 through 925 Processing helix chain 'D' and resid 930 through 939 removed outlier: 3.824A pdb=" N LYS D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 962 removed outlier: 3.662A pdb=" N VAL D 945 " --> pdb=" O GLU D 941 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 962 " --> pdb=" O MET D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 985 Processing helix chain 'D' and resid 985 through 991 removed outlier: 4.128A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 997 through 1033 removed outlier: 3.575A pdb=" N ILE D1016 " --> pdb=" O TYR D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1054 removed outlier: 3.616A pdb=" N ILE D1046 " --> pdb=" O LEU D1042 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE D1047 " --> pdb=" O ALA D1043 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET D1049 " --> pdb=" O ASN D1045 " (cutoff:3.500A) Proline residue: D1050 - end of helix removed outlier: 3.661A pdb=" N ILE D1054 " --> pdb=" O PRO D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1105 removed outlier: 4.230A pdb=" N ALA D1093 " --> pdb=" O TRP D1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 1105 through 1117 Processing helix chain 'D' and resid 1118 through 1142 removed outlier: 4.541A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.350A 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 1161 removed outlier: 3.553A pdb=" N MET D1158 " --> pdb=" O SER D1154 " (cutoff:3.500A) Processing helix chain 'D' and resid 1162 through 1164 No H-bonds generated for 'chain 'D' and resid 1162 through 1164' Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 275 removed outlier: 7.014A pdb=" N PHE A 141 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG A 272 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR A 143 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR A 274 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU A 145 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N PHE A 294 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET A 156 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU A 296 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 158 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASP A 298 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 160 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR A 250 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE A 295 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY A 252 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA A 297 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 254 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 220 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE A 253 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A 222 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 186 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 185 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 337 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N VAL A 362 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA A 336 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N CYS A 364 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 275 removed outlier: 7.013A pdb=" N PHE B 141 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ARG B 272 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B 143 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR B 274 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU B 145 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE B 294 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 156 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU B 296 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 158 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASP B 298 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL B 160 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR B 250 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE B 295 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE B 220 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE B 253 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR B 222 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 186 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER B 187 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N VAL B 362 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 336 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N CYS B 364 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AA6, first strand: chain 'C' and resid 270 through 275 removed outlier: 7.013A pdb=" N PHE C 141 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ARG C 272 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR C 143 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR C 274 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C 145 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE C 294 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET C 156 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU C 296 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 158 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASP C 298 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL C 160 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR C 250 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE C 295 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY C 252 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA C 297 " --> pdb=" O GLY C 252 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA C 254 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE C 220 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE C 253 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR C 222 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE C 186 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU C 185 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 337 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER C 187 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N VAL C 362 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 336 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N CYS C 364 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'D' and resid 270 through 275 removed outlier: 7.013A pdb=" N PHE D 141 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG D 272 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR D 143 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR D 274 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU D 145 " --> pdb=" O TYR D 274 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE D 294 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET D 156 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU D 296 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL D 158 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASP D 298 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL D 160 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR D 250 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE D 295 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY D 252 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA D 297 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA D 254 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE D 220 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE D 253 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR D 222 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE D 186 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU D 185 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU D 337 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER D 187 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N VAL D 362 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA D 336 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N CYS D 364 " --> pdb=" O ALA D 336 " (cutoff:3.500A) 1735 hydrogen bonds defined for protein. 5133 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: 6.74 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 16 1.05 - 1.26: 5064 1.26 - 1.47: 13051 1.47 - 1.69: 14409 1.69 - 1.90: 428 Bond restraints: 32968 Sorted by residual: bond pdb=" C03 9Z9 C1402 " pdb=" C74 9Z9 C1402 " ideal model delta sigma weight residual 1.534 0.836 0.698 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C03 9Z9 D1402 " pdb=" C74 9Z9 D1402 " ideal model delta sigma weight residual 1.534 0.836 0.698 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C03 9Z9 B1402 " pdb=" C74 9Z9 B1402 " ideal model delta sigma weight residual 1.534 0.837 0.697 2.00e-02 2.50e+03 1.21e+03 bond pdb=" C03 9Z9 A1402 " pdb=" C74 9Z9 A1402 " ideal model delta sigma weight residual 1.534 0.838 0.696 2.00e-02 2.50e+03 1.21e+03 bond pdb=" C02 9Z9 B1402 " pdb=" C03 9Z9 B1402 " ideal model delta sigma weight residual 1.544 1.014 0.530 2.00e-02 2.50e+03 7.01e+02 ... (remaining 32963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.53: 44552 10.53 - 21.06: 16 21.06 - 31.59: 8 31.59 - 42.12: 4 42.12 - 52.64: 4 Bond angle restraints: 44584 Sorted by residual: angle pdb=" C74 9Z9 C1402 " pdb=" C73 9Z9 C1402 " pdb=" C76 9Z9 C1402 " ideal model delta sigma weight residual 114.05 166.69 -52.64 3.00e+00 1.11e-01 3.08e+02 angle pdb=" C74 9Z9 B1402 " pdb=" C73 9Z9 B1402 " pdb=" C76 9Z9 B1402 " ideal model delta sigma weight residual 114.05 166.69 -52.64 3.00e+00 1.11e-01 3.08e+02 angle pdb=" C74 9Z9 A1402 " pdb=" C73 9Z9 A1402 " pdb=" C76 9Z9 A1402 " ideal model delta sigma weight residual 114.05 166.63 -52.58 3.00e+00 1.11e-01 3.07e+02 angle pdb=" C74 9Z9 D1402 " pdb=" C73 9Z9 D1402 " pdb=" C76 9Z9 D1402 " ideal model delta sigma weight residual 114.05 166.63 -52.58 3.00e+00 1.11e-01 3.07e+02 angle pdb=" C76 9Z9 D1402 " pdb=" C73 9Z9 D1402 " pdb=" O72 9Z9 D1402 " ideal model delta sigma weight residual 109.02 71.91 37.11 3.00e+00 1.11e-01 1.53e+02 ... (remaining 44579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 18700 21.87 - 43.75: 779 43.75 - 65.62: 168 65.62 - 87.50: 4 87.50 - 109.37: 4 Dihedral angle restraints: 19655 sinusoidal: 8163 harmonic: 11492 Sorted by residual: dihedral pdb=" CA THR C 356 " pdb=" C THR C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA THR B 356 " pdb=" C THR B 356 " pdb=" N PRO B 357 " pdb=" CA PRO B 357 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 19652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.375: 4968 0.375 - 0.751: 4 0.751 - 1.126: 4 1.126 - 1.501: 0 1.501 - 1.877: 4 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C03 9Z9 D1402 " pdb=" C02 9Z9 D1402 " pdb=" C04 9Z9 D1402 " pdb=" C74 9Z9 D1402 " both_signs ideal model delta sigma weight residual False 2.78 0.90 1.88 2.00e-01 2.50e+01 8.81e+01 chirality pdb=" C03 9Z9 C1402 " pdb=" C02 9Z9 C1402 " pdb=" C04 9Z9 C1402 " pdb=" C74 9Z9 C1402 " both_signs ideal model delta sigma weight residual False 2.78 0.90 1.88 2.00e-01 2.50e+01 8.81e+01 chirality pdb=" C03 9Z9 B1402 " pdb=" C02 9Z9 B1402 " pdb=" C04 9Z9 B1402 " pdb=" C74 9Z9 B1402 " both_signs ideal model delta sigma weight residual False 2.78 0.90 1.88 2.00e-01 2.50e+01 8.80e+01 ... (remaining 4977 not shown) Planarity restraints: 5516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 784 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO C 785 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 785 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 785 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 784 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO B 785 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 785 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 785 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 784 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO D 785 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 785 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 785 " -0.031 5.00e-02 4.00e+02 ... (remaining 5513 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6860 2.78 - 3.31: 30650 3.31 - 3.84: 50763 3.84 - 4.37: 57613 4.37 - 4.90: 103912 Nonbonded interactions: 249798 Sorted by model distance: nonbonded pdb=" OE2 GLU A 565 " pdb=" OG1 THR A 577 " model vdw 2.252 3.040 nonbonded pdb=" OE2 GLU D 565 " pdb=" OG1 THR D 577 " model vdw 2.252 3.040 nonbonded pdb=" OE2 GLU B 565 " pdb=" OG1 THR B 577 " model vdw 2.253 3.040 nonbonded pdb=" OE2 GLU C 565 " pdb=" OG1 THR C 577 " model vdw 2.253 3.040 nonbonded pdb=" OG SER D 187 " pdb=" OE2 GLU D 316 " model vdw 2.275 3.040 ... (remaining 249793 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 1403) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.320 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 0.698 32968 Z= 0.750 Angle : 1.022 52.645 44584 Z= 0.405 Chirality : 0.075 1.877 4980 Planarity : 0.004 0.054 5516 Dihedral : 12.020 109.371 12223 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.75 % Allowed : 6.17 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3824 helix: 1.56 (0.11), residues: 2380 sheet: 0.36 (0.38), residues: 212 loop : -1.80 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 313 TYR 0.014 0.001 TYR D1048 PHE 0.011 0.001 PHE A1013 TRP 0.013 0.001 TRP A 763 HIS 0.002 0.001 HIS D 633 Details of bonding type rmsd/Z covalent geometry : bond 0.01508 / 0.75 (32968) covalent geometry : angle 1.02206 / 0.40 (44584) hydrogen bonds : bond 0.16380 / 11.00 ( 1735) hydrogen bonds : angle 4.65536 / 3.25 ( 5133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 655 time to evaluate : 1.160 Fit side-chains REVERT: A 313 ARG cc_start: 0.7276 (tpt170) cc_final: 0.7064 (mmm160) REVERT: A 920 MET cc_start: 0.7197 (mtt) cc_final: 0.6960 (mtm) REVERT: A 1207 GLU cc_start: 0.7232 (tp30) cc_final: 0.6990 (tp30) REVERT: B 313 ARG cc_start: 0.7280 (tpt170) cc_final: 0.7066 (mmm160) REVERT: B 920 MET cc_start: 0.7234 (mtt) cc_final: 0.6986 (mtm) REVERT: B 1207 GLU cc_start: 0.7241 (tp30) cc_final: 0.6970 (tp30) REVERT: C 269 ASP cc_start: 0.7123 (t70) cc_final: 0.6887 (t70) REVERT: C 1207 GLU cc_start: 0.7239 (tp30) cc_final: 0.6953 (tp30) REVERT: D 313 ARG cc_start: 0.7302 (tpt170) cc_final: 0.7081 (mmm160) REVERT: D 1207 GLU cc_start: 0.7234 (tp30) cc_final: 0.6961 (tp30) outliers start: 60 outliers final: 24 residues processed: 698 average time/residue: 0.6044 time to fit residues: 499.9336 Evaluate side-chains 499 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 475 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1014 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 291 HIS A 314 GLN A 575 ASN A 586 HIS A 697 HIS A 746 HIS A 794 ASN A 978 ASN A1035 ASN A1115 ASN A1238 ASN B 171 HIS B 291 HIS B 314 GLN B 575 ASN B 586 HIS B 746 HIS B 794 ASN B 978 ASN B1035 ASN B1115 ASN B1238 ASN C 171 HIS C 291 HIS C 314 GLN C 575 ASN C 586 HIS C 697 HIS C 746 HIS C 794 ASN C 978 ASN C1035 ASN C1115 ASN C1238 ASN D 171 HIS D 291 HIS D 314 GLN D 575 ASN D 586 HIS D 746 HIS D 978 ASN D1035 ASN D1115 ASN D1238 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124667 restraints weight = 37715.302| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.28 r_work: 0.3148 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 32968 Z= 0.284 Angle : 0.678 9.436 44584 Z= 0.340 Chirality : 0.044 0.157 4980 Planarity : 0.005 0.045 5516 Dihedral : 8.626 95.162 4532 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.66 % Allowed : 12.37 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 3824 helix: 1.35 (0.10), residues: 2412 sheet: 0.16 (0.37), residues: 208 loop : -2.02 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 972 TYR 0.016 0.002 TYR A 885 PHE 0.015 0.002 PHE C 503 TRP 0.020 0.002 TRP B 763 HIS 0.004 0.001 HIS C 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.28 (32968) covalent geometry : angle 0.67828 / 0.34 (44584) hydrogen bonds : bond 0.07813 / 5.27 ( 1735) hydrogen bonds : angle 3.93427 / 2.77 ( 5133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 504 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 175 LYS cc_start: 0.8110 (mppt) cc_final: 0.7834 (mtmm) REVERT: A 266 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7176 (mm) REVERT: A 269 ASP cc_start: 0.7608 (t70) cc_final: 0.7087 (t70) REVERT: A 354 ARG cc_start: 0.7648 (mtm-85) cc_final: 0.7255 (mtm110) REVERT: A 374 LEU cc_start: 0.7354 (mt) cc_final: 0.6892 (mt) REVERT: A 418 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.6330 (tmm) REVERT: A 722 MET cc_start: 0.9040 (mtt) cc_final: 0.8725 (mtt) REVERT: A 730 LYS cc_start: 0.9093 (mmtp) cc_final: 0.8733 (mmtm) REVERT: A 1115 ASN cc_start: 0.9126 (OUTLIER) cc_final: 0.8881 (t0) REVERT: A 1138 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8276 (mmt) REVERT: A 1207 GLU cc_start: 0.8554 (tp30) cc_final: 0.8314 (tm-30) REVERT: A 1232 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7311 (mpp) REVERT: B 165 LYS cc_start: 0.7435 (mmtp) cc_final: 0.7170 (ttmm) REVERT: B 266 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7273 (mm) REVERT: B 269 ASP cc_start: 0.7718 (t70) cc_final: 0.7146 (t70) REVERT: B 354 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7201 (mtm110) REVERT: B 374 LEU cc_start: 0.7312 (mt) cc_final: 0.6889 (mt) REVERT: B 418 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.6332 (tmm) REVERT: B 722 MET cc_start: 0.9039 (mtt) cc_final: 0.8725 (mtt) REVERT: B 730 LYS cc_start: 0.9093 (mmtp) cc_final: 0.8741 (mmtm) REVERT: B 1115 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8857 (t0) REVERT: B 1138 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8254 (mmt) REVERT: B 1207 GLU cc_start: 0.8550 (tp30) cc_final: 0.8299 (tm-30) REVERT: B 1232 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7351 (mpp) REVERT: C 266 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7277 (mm) REVERT: C 269 ASP cc_start: 0.7737 (t70) cc_final: 0.7174 (t70) REVERT: C 354 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7374 (mtm-85) REVERT: C 374 LEU cc_start: 0.7313 (mt) cc_final: 0.6976 (mt) REVERT: C 418 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7140 (pmm) REVERT: C 722 MET cc_start: 0.9045 (mtt) cc_final: 0.8732 (mtt) REVERT: C 730 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8729 (mmtm) REVERT: C 1115 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8893 (t0) REVERT: C 1138 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8231 (mmt) REVERT: C 1207 GLU cc_start: 0.8559 (tp30) cc_final: 0.8306 (tm-30) REVERT: C 1232 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7401 (mpp) REVERT: D 176 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6333 (tp30) REVERT: D 266 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7254 (mm) REVERT: D 269 ASP cc_start: 0.7710 (t70) cc_final: 0.7128 (t70) REVERT: D 354 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7212 (mtm110) REVERT: D 374 LEU cc_start: 0.7418 (mt) cc_final: 0.7037 (mt) REVERT: D 418 MET cc_start: 0.7742 (ptp) cc_final: 0.6931 (pmm) REVERT: D 722 MET cc_start: 0.9039 (mtt) cc_final: 0.8722 (mtt) REVERT: D 1115 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8850 (t0) REVERT: D 1138 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8261 (mmt) REVERT: D 1207 GLU cc_start: 0.8571 (tp30) cc_final: 0.8328 (tm-30) REVERT: D 1232 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7307 (mpp) outliers start: 160 outliers final: 51 residues processed: 604 average time/residue: 0.5753 time to fit residues: 414.4650 Evaluate side-chains 542 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 471 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1232 MET Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1232 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 70 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 195 optimal weight: 7.9990 chunk 343 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 332 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 240 HIS A 314 GLN A 586 HIS A 716 GLN A 978 ASN A1035 ASN A1115 ASN A1116 ASN B 171 HIS B 240 HIS B 314 GLN B 586 HIS B 716 GLN B 978 ASN B1035 ASN B1115 ASN B1116 ASN C 171 HIS C 240 HIS C 314 GLN C 586 HIS C 716 GLN C 978 ASN C1035 ASN C1115 ASN C1116 ASN D 171 HIS D 240 HIS D 314 GLN D 586 HIS D 716 GLN D 978 ASN D1035 ASN D1115 ASN D1116 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.171110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130110 restraints weight = 37441.157| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.38 r_work: 0.3230 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32968 Z= 0.125 Angle : 0.533 7.807 44584 Z= 0.265 Chirality : 0.038 0.136 4980 Planarity : 0.004 0.041 5516 Dihedral : 8.202 83.673 4528 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.13 % Allowed : 14.41 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.14), residues: 3824 helix: 1.90 (0.11), residues: 2412 sheet: 0.28 (0.37), residues: 208 loop : -1.89 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 700 TYR 0.015 0.001 TYR B 981 PHE 0.008 0.001 PHE C1013 TRP 0.012 0.001 TRP B 763 HIS 0.004 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (32968) covalent geometry : angle 0.53281 / 0.27 (44584) hydrogen bonds : bond 0.05603 / 3.79 ( 1735) hydrogen bonds : angle 3.59782 / 2.53 ( 5133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 521 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7989 (p90) cc_final: 0.7763 (p90) REVERT: A 264 ASP cc_start: 0.6279 (OUTLIER) cc_final: 0.5528 (m-30) REVERT: A 266 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7267 (mm) REVERT: A 354 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.7137 (mtp-110) REVERT: A 374 LEU cc_start: 0.7168 (mt) cc_final: 0.6798 (mt) REVERT: A 418 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7089 (pmm) REVERT: A 462 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8267 (mp) REVERT: A 546 LYS cc_start: 0.7508 (mmmt) cc_final: 0.7263 (mmtm) REVERT: A 642 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8110 (tpt) REVERT: A 722 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8609 (mtt) REVERT: A 963 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7342 (mp10) REVERT: A 1011 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.6689 (mmp) REVERT: A 1053 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8413 (ttm) REVERT: A 1138 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8235 (mmm) REVERT: A 1207 GLU cc_start: 0.8460 (tp30) cc_final: 0.7976 (tp30) REVERT: B 162 PHE cc_start: 0.7988 (p90) cc_final: 0.7770 (p90) REVERT: B 266 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7271 (mm) REVERT: B 354 ARG cc_start: 0.7450 (mtm-85) cc_final: 0.7098 (mtp-110) REVERT: B 374 LEU cc_start: 0.7133 (mt) cc_final: 0.6759 (mt) REVERT: B 418 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7106 (pmm) REVERT: B 462 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8277 (mp) REVERT: B 546 LYS cc_start: 0.7489 (mmmt) cc_final: 0.7241 (mmtm) REVERT: B 642 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8132 (tpt) REVERT: B 722 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8615 (mtt) REVERT: B 963 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7350 (mp10) REVERT: B 1007 MET cc_start: 0.7982 (mtp) cc_final: 0.7773 (mtp) REVERT: B 1011 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.6639 (mmp) REVERT: B 1138 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8227 (mmm) REVERT: B 1207 GLU cc_start: 0.8459 (tp30) cc_final: 0.8210 (tm-30) REVERT: C 162 PHE cc_start: 0.7983 (p90) cc_final: 0.7762 (p90) REVERT: C 266 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7266 (mm) REVERT: C 350 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7793 (tm) REVERT: C 354 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7151 (mtp-110) REVERT: C 374 LEU cc_start: 0.7237 (mt) cc_final: 0.6894 (mt) REVERT: C 418 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7120 (pmm) REVERT: C 462 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8262 (mp) REVERT: C 546 LYS cc_start: 0.7434 (mmmt) cc_final: 0.7169 (mmtm) REVERT: C 642 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8127 (tpt) REVERT: C 722 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8613 (mtt) REVERT: C 1011 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.6639 (mmp) REVERT: C 1138 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8222 (mmm) REVERT: C 1207 GLU cc_start: 0.8435 (tp30) cc_final: 0.8194 (tm-30) REVERT: C 1234 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8435 (tm) REVERT: D 162 PHE cc_start: 0.7996 (p90) cc_final: 0.7778 (p90) REVERT: D 266 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7265 (mm) REVERT: D 354 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.7086 (mtp-110) REVERT: D 374 LEU cc_start: 0.7117 (mt) cc_final: 0.6766 (mt) REVERT: D 462 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8273 (mp) REVERT: D 546 LYS cc_start: 0.7491 (mmmt) cc_final: 0.7249 (mmtm) REVERT: D 642 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8123 (tpt) REVERT: D 722 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8609 (mtt) REVERT: D 1011 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.6642 (mmp) REVERT: D 1138 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8200 (mmm) REVERT: D 1207 GLU cc_start: 0.8460 (tp30) cc_final: 0.8206 (tm-30) outliers start: 142 outliers final: 51 residues processed: 603 average time/residue: 0.6059 time to fit residues: 436.5441 Evaluate side-chains 543 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 459 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 963 GLN Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1202 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 276 THR 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 416 ILE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 67 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 ASN A 171 HIS A 240 HIS A 314 GLN A 586 HIS ** A 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN A 978 ASN A1035 ASN A1115 ASN ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN B 171 HIS B 240 HIS B 314 GLN B 586 HIS ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN B 978 ASN B1035 ASN B1115 ASN ** B1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 171 HIS C 240 HIS C 314 GLN C 586 HIS ** C 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 734 ASN C 978 ASN C1035 ASN C1115 ASN ** C1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN D 171 HIS D 240 HIS D 314 GLN D 586 HIS ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 734 ASN D 794 ASN D 978 ASN D1035 ASN D1115 ASN ** D1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118845 restraints weight = 37875.306| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.51 r_work: 0.3079 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.073 32968 Z= 0.404 Angle : 0.771 9.479 44584 Z= 0.389 Chirality : 0.049 0.210 4980 Planarity : 0.005 0.060 5516 Dihedral : 8.621 71.717 4528 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.74 % Allowed : 14.56 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 3824 helix: 1.11 (0.10), residues: 2420 sheet: -0.17 (0.35), residues: 216 loop : -2.25 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1240 TYR 0.020 0.002 TYR D 885 PHE 0.017 0.002 PHE D 503 TRP 0.023 0.003 TRP A 763 HIS 0.007 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.01008 / 0.40 (32968) covalent geometry : angle 0.77063 / 0.39 (44584) hydrogen bonds : bond 0.09105 / 6.14 ( 1735) hydrogen bonds : angle 4.06436 / 2.86 ( 5133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 479 time to evaluate : 1.177 Fit side-chains REVERT: A 193 GLN cc_start: 0.7475 (mp10) cc_final: 0.6983 (mm-40) REVERT: A 266 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.6886 (mm) REVERT: A 269 ASP cc_start: 0.7551 (t70) cc_final: 0.7043 (t70) REVERT: A 354 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.7397 (mtm110) REVERT: A 374 LEU cc_start: 0.7195 (mt) cc_final: 0.6833 (mt) REVERT: A 418 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7173 (pmm) REVERT: A 530 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8296 (mmp80) REVERT: A 722 MET cc_start: 0.9083 (mtt) cc_final: 0.8801 (mtt) REVERT: A 963 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: A 1007 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8375 (mtp) REVERT: A 1053 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8452 (ttm) REVERT: A 1115 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8954 (t0) REVERT: A 1138 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8276 (mmt) REVERT: A 1142 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: A 1181 LEU cc_start: 0.7149 (mp) cc_final: 0.6941 (mt) REVERT: A 1207 GLU cc_start: 0.8507 (tp30) cc_final: 0.8211 (tm-30) REVERT: B 193 GLN cc_start: 0.7434 (mp10) cc_final: 0.6931 (mm-40) REVERT: B 266 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.6886 (mm) REVERT: B 269 ASP cc_start: 0.7712 (t70) cc_final: 0.7163 (t70) REVERT: B 354 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7383 (mtm110) REVERT: B 374 LEU cc_start: 0.7279 (mt) cc_final: 0.6857 (mt) REVERT: B 418 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7197 (pmm) REVERT: B 530 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8267 (mmp80) REVERT: B 722 MET cc_start: 0.9086 (mtt) cc_final: 0.8806 (mtt) REVERT: B 1115 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8957 (t0) REVERT: B 1138 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8276 (mmt) REVERT: B 1142 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: B 1181 LEU cc_start: 0.7138 (mp) cc_final: 0.6928 (mt) REVERT: B 1207 GLU cc_start: 0.8455 (tp30) cc_final: 0.8169 (tm-30) REVERT: C 193 GLN cc_start: 0.7468 (mp10) cc_final: 0.6969 (mm-40) REVERT: C 266 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.6890 (mm) REVERT: C 269 ASP cc_start: 0.7719 (t70) cc_final: 0.7166 (t70) REVERT: C 287 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7826 (mp) REVERT: C 354 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7348 (mtm110) REVERT: C 374 LEU cc_start: 0.7216 (mt) cc_final: 0.6882 (mt) REVERT: C 418 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7132 (pmm) REVERT: C 722 MET cc_start: 0.9097 (mtt) cc_final: 0.8822 (mtt) REVERT: C 1007 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8362 (mtp) REVERT: C 1115 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8955 (t0) REVERT: C 1181 LEU cc_start: 0.7110 (mp) cc_final: 0.6833 (mt) REVERT: C 1207 GLU cc_start: 0.8462 (tp30) cc_final: 0.8170 (tm-30) REVERT: C 1234 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8224 (tm) REVERT: D 193 GLN cc_start: 0.7463 (mp10) cc_final: 0.6954 (mm-40) REVERT: D 266 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.6855 (mm) REVERT: D 269 ASP cc_start: 0.7716 (t70) cc_final: 0.7161 (t70) REVERT: D 354 ARG cc_start: 0.7614 (mtm-85) cc_final: 0.7386 (mtm110) REVERT: D 374 LEU cc_start: 0.7231 (mt) cc_final: 0.6869 (mt) REVERT: D 530 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8303 (mmp80) REVERT: D 722 MET cc_start: 0.9092 (mtt) cc_final: 0.8814 (mtt) REVERT: D 1007 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8361 (mtp) REVERT: D 1115 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8944 (t0) REVERT: D 1138 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8327 (mmt) REVERT: D 1207 GLU cc_start: 0.8463 (tp30) cc_final: 0.8174 (tm-30) REVERT: D 1232 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7353 (mpp) outliers start: 197 outliers final: 84 residues processed: 602 average time/residue: 0.6154 time to fit residues: 444.1723 Evaluate side-chains 572 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 461 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 ARG Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 530 ARG Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1142 GLU Chi-restraints excluded: chain B residue 1202 GLU Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 1007 MET Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 530 ARG Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1007 MET Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1202 GLU Chi-restraints excluded: chain D residue 1227 VAL Chi-restraints excluded: chain D residue 1232 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 242 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 338 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 375 optimal weight: 0.5980 chunk 263 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 284 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 314 GLN A 586 HIS A 739 GLN A 978 ASN A1115 ASN B 171 HIS B 314 GLN B 586 HIS B 739 GLN B 978 ASN B1115 ASN C 171 HIS C 314 GLN C 586 HIS C 739 GLN C 978 ASN C1115 ASN D 171 HIS D 314 GLN D 586 HIS D 734 ASN ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 978 ASN D1115 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.170009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117845 restraints weight = 37450.346| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.18 r_work: 0.3178 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32968 Z= 0.136 Angle : 0.563 8.462 44584 Z= 0.281 Chirality : 0.039 0.142 4980 Planarity : 0.004 0.041 5516 Dihedral : 8.166 67.567 4528 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.89 % Allowed : 16.62 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3824 helix: 1.64 (0.11), residues: 2420 sheet: 0.02 (0.36), residues: 204 loop : -1.99 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 354 TYR 0.017 0.001 TYR C 981 PHE 0.012 0.001 PHE A 162 TRP 0.013 0.001 TRP B 763 HIS 0.007 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (32968) covalent geometry : angle 0.56292 / 0.28 (44584) hydrogen bonds : bond 0.05976 / 4.04 ( 1735) hydrogen bonds : angle 3.66362 / 2.58 ( 5133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 493 time to evaluate : 1.146 Fit side-chains REVERT: A 162 PHE cc_start: 0.8025 (p90) cc_final: 0.7824 (p90) REVERT: A 263 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6863 (pp20) REVERT: A 269 ASP cc_start: 0.7564 (t70) cc_final: 0.7046 (t70) REVERT: A 374 LEU cc_start: 0.7011 (mt) cc_final: 0.6720 (mt) REVERT: A 418 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7174 (pmm) REVERT: A 462 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8013 (mp) REVERT: A 482 GLN cc_start: 0.6526 (mp10) cc_final: 0.6312 (tm-30) REVERT: A 722 MET cc_start: 0.8941 (mtt) cc_final: 0.8607 (mtt) REVERT: A 932 LEU cc_start: 0.6519 (tm) cc_final: 0.6310 (tp) REVERT: A 963 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: A 1011 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.6511 (mmt) REVERT: A 1053 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8348 (ttm) REVERT: A 1138 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8174 (mmt) REVERT: A 1142 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: A 1207 GLU cc_start: 0.8290 (tp30) cc_final: 0.8008 (tm-30) REVERT: A 1234 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8089 (tm) REVERT: B 266 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6777 (mm) REVERT: B 269 ASP cc_start: 0.7599 (t70) cc_final: 0.7067 (t70) REVERT: B 374 LEU cc_start: 0.7022 (mt) cc_final: 0.6722 (mt) REVERT: B 418 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7131 (pmm) REVERT: B 462 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8047 (mp) REVERT: B 722 MET cc_start: 0.8939 (mtt) cc_final: 0.8606 (mtt) REVERT: B 1001 MET cc_start: 0.8643 (mmm) cc_final: 0.8244 (mtm) REVERT: B 1011 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.6547 (mmt) REVERT: B 1138 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8163 (mmt) REVERT: B 1207 GLU cc_start: 0.8286 (tp30) cc_final: 0.7999 (tm-30) REVERT: B 1234 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8148 (tm) REVERT: C 193 GLN cc_start: 0.7374 (mp10) cc_final: 0.6871 (mm-40) REVERT: C 266 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.6782 (mm) REVERT: C 269 ASP cc_start: 0.7608 (t70) cc_final: 0.7079 (t70) REVERT: C 354 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7305 (mtm110) REVERT: C 374 LEU cc_start: 0.7097 (mt) cc_final: 0.6793 (mt) REVERT: C 418 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7108 (pmm) REVERT: C 462 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8052 (mp) REVERT: C 722 MET cc_start: 0.8940 (mtt) cc_final: 0.8608 (mtt) REVERT: C 932 LEU cc_start: 0.6515 (tm) cc_final: 0.6310 (tp) REVERT: C 1011 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.6540 (mmt) REVERT: C 1138 MET cc_start: 0.8395 (mmt) cc_final: 0.8175 (mmm) REVERT: C 1207 GLU cc_start: 0.8303 (tp30) cc_final: 0.8016 (tm-30) REVERT: C 1234 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8166 (tm) REVERT: D 269 ASP cc_start: 0.7601 (t70) cc_final: 0.7065 (t70) REVERT: D 374 LEU cc_start: 0.6847 (mt) cc_final: 0.6551 (mt) REVERT: D 462 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8041 (mp) REVERT: D 722 MET cc_start: 0.8955 (mtt) cc_final: 0.8629 (mtt) REVERT: D 932 LEU cc_start: 0.6511 (tm) cc_final: 0.6302 (tp) REVERT: D 1011 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.6543 (mmt) REVERT: D 1138 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8226 (mmt) REVERT: D 1207 GLU cc_start: 0.8298 (tp30) cc_final: 0.8010 (tm-30) outliers start: 168 outliers final: 51 residues processed: 594 average time/residue: 0.5722 time to fit residues: 409.9027 Evaluate side-chains 545 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 471 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1202 GLU Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 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 397 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 275 optimal weight: 0.0970 chunk 113 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 198 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 359 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 240 HIS A 314 GLN A 586 HIS A 978 ASN A1035 ASN A1115 ASN B 171 HIS B 240 HIS B 314 GLN B 586 HIS B 978 ASN B1035 ASN B1115 ASN C 171 HIS C 240 HIS C 314 GLN C 586 HIS C 978 ASN C1035 ASN C1115 ASN D 171 HIS D 240 HIS D 314 GLN D 586 HIS ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 978 ASN D1035 ASN D1115 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.168681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123153 restraints weight = 37379.453| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.47 r_work: 0.3158 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32968 Z= 0.183 Angle : 0.586 7.842 44584 Z= 0.289 Chirality : 0.040 0.156 4980 Planarity : 0.004 0.040 5516 Dihedral : 7.952 62.144 4528 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.86 % Allowed : 16.83 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3824 helix: 1.67 (0.11), residues: 2416 sheet: 0.02 (0.36), residues: 204 loop : -2.01 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 354 TYR 0.015 0.001 TYR B 865 PHE 0.014 0.001 PHE D 162 TRP 0.015 0.001 TRP D 763 HIS 0.005 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (32968) covalent geometry : angle 0.58581 / 0.29 (44584) hydrogen bonds : bond 0.06460 / 4.36 ( 1735) hydrogen bonds : angle 3.64234 / 2.56 ( 5133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 491 time to evaluate : 1.220 Fit side-chains REVERT: A 162 PHE cc_start: 0.7978 (p90) cc_final: 0.7752 (p90) REVERT: A 263 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6584 (pp20) REVERT: A 264 ASP cc_start: 0.6093 (OUTLIER) cc_final: 0.5692 (m-30) REVERT: A 269 ASP cc_start: 0.7527 (t70) cc_final: 0.7015 (t70) REVERT: A 374 LEU cc_start: 0.7060 (mt) cc_final: 0.6792 (mt) REVERT: A 418 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7088 (pmm) REVERT: A 462 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 722 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8508 (mtt) REVERT: A 932 LEU cc_start: 0.6630 (tm) cc_final: 0.6426 (tp) REVERT: A 963 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: A 1011 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.6629 (mmt) REVERT: A 1053 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8319 (ttm) REVERT: A 1057 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6360 (tt0) REVERT: A 1061 ASP cc_start: 0.8246 (m-30) cc_final: 0.7839 (m-30) REVERT: A 1138 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8039 (mmt) REVERT: A 1142 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: A 1207 GLU cc_start: 0.8177 (tp30) cc_final: 0.7580 (tp30) REVERT: A 1232 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7122 (mpp) REVERT: A 1234 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8211 (tm) REVERT: B 269 ASP cc_start: 0.7596 (t70) cc_final: 0.7058 (t70) REVERT: B 374 LEU cc_start: 0.7080 (mt) cc_final: 0.6779 (mt) REVERT: B 418 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7088 (pmm) REVERT: B 462 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7955 (mp) REVERT: B 722 MET cc_start: 0.8865 (mtt) cc_final: 0.8516 (mtt) REVERT: B 932 LEU cc_start: 0.6630 (tm) cc_final: 0.6419 (tp) REVERT: B 1011 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.6658 (mmt) REVERT: B 1057 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6404 (tt0) REVERT: B 1061 ASP cc_start: 0.8201 (m-30) cc_final: 0.7801 (m-30) REVERT: B 1138 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8074 (mmt) REVERT: B 1142 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: B 1207 GLU cc_start: 0.8183 (tp30) cc_final: 0.7904 (tm-30) REVERT: B 1232 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7166 (mpp) REVERT: B 1234 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8166 (tm) REVERT: C 170 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8331 (OUTLIER) REVERT: C 193 GLN cc_start: 0.7334 (mp10) cc_final: 0.6846 (mm-40) REVERT: C 269 ASP cc_start: 0.7603 (t70) cc_final: 0.7067 (t70) REVERT: C 354 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.7131 (mtp-110) REVERT: C 374 LEU cc_start: 0.7133 (mt) cc_final: 0.6873 (mt) REVERT: C 418 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7014 (pmm) REVERT: C 462 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7924 (mp) REVERT: C 722 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8523 (mtt) REVERT: C 1001 MET cc_start: 0.8381 (mtt) cc_final: 0.7910 (mtm) REVERT: C 1011 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.6649 (mmt) REVERT: C 1057 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6333 (tt0) REVERT: C 1061 ASP cc_start: 0.8243 (m-30) cc_final: 0.7848 (m-30) REVERT: C 1138 MET cc_start: 0.8271 (mmt) cc_final: 0.8041 (mmm) REVERT: C 1207 GLU cc_start: 0.8188 (tp30) cc_final: 0.7905 (tm-30) REVERT: C 1232 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7159 (mpp) REVERT: C 1234 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8238 (tm) REVERT: D 193 GLN cc_start: 0.7365 (mp10) cc_final: 0.6864 (mm-40) REVERT: D 266 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.6953 (mm) REVERT: D 269 ASP cc_start: 0.7591 (t70) cc_final: 0.7050 (t70) REVERT: D 287 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7777 (mp) REVERT: D 374 LEU cc_start: 0.7015 (mt) cc_final: 0.6715 (mt) REVERT: D 462 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7931 (mp) REVERT: D 722 MET cc_start: 0.8884 (mtt) cc_final: 0.8540 (mtt) REVERT: D 932 LEU cc_start: 0.6678 (tm) cc_final: 0.6472 (tp) REVERT: D 1001 MET cc_start: 0.8388 (mtt) cc_final: 0.7913 (mtm) REVERT: D 1011 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.6654 (mmt) REVERT: D 1057 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6335 (tt0) REVERT: D 1061 ASP cc_start: 0.8224 (m-30) cc_final: 0.7823 (m-30) REVERT: D 1138 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8085 (mmt) REVERT: D 1207 GLU cc_start: 0.8179 (tp30) cc_final: 0.7898 (tm-30) outliers start: 167 outliers final: 68 residues processed: 598 average time/residue: 0.5695 time to fit residues: 409.6423 Evaluate side-chains 574 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 472 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1057 GLU Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1142 GLU Chi-restraints excluded: chain B residue 1202 GLU Chi-restraints excluded: chain B residue 1232 MET Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 1007 MET Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1057 GLU Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1007 MET Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1057 GLU Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 286 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 329 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 316 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 314 GLN A 586 HIS A 978 ASN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 314 GLN B 586 HIS B 978 ASN ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 314 GLN C 586 HIS C 978 ASN ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 HIS ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 978 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.166719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122425 restraints weight = 37647.930| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.49 r_work: 0.3125 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 32968 Z= 0.246 Angle : 0.635 6.897 44584 Z= 0.318 Chirality : 0.043 0.172 4980 Planarity : 0.004 0.042 5516 Dihedral : 7.975 59.409 4528 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.51 % Allowed : 17.47 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3824 helix: 1.49 (0.11), residues: 2420 sheet: -0.01 (0.36), residues: 204 loop : -2.09 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 354 TYR 0.016 0.002 TYR C 865 PHE 0.016 0.002 PHE C 162 TRP 0.018 0.002 TRP C 763 HIS 0.005 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.25 (32968) covalent geometry : angle 0.63515 / 0.32 (44584) hydrogen bonds : bond 0.07324 / 4.94 ( 1735) hydrogen bonds : angle 3.76682 / 2.65 ( 5133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 484 time to evaluate : 1.112 Fit side-chains REVERT: A 264 ASP cc_start: 0.6188 (OUTLIER) cc_final: 0.5971 (m-30) REVERT: A 269 ASP cc_start: 0.7594 (t70) cc_final: 0.7075 (t70) REVERT: A 374 LEU cc_start: 0.7083 (mt) cc_final: 0.6806 (mt) REVERT: A 418 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7083 (pmm) REVERT: A 462 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7945 (mp) REVERT: A 530 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8147 (mmp80) REVERT: A 722 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8561 (mtt) REVERT: A 963 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7674 (mp10) REVERT: A 1053 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8325 (ttm) REVERT: A 1057 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: A 1061 ASP cc_start: 0.8249 (m-30) cc_final: 0.7841 (m-30) REVERT: A 1138 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8052 (mmt) REVERT: A 1142 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: A 1207 GLU cc_start: 0.8208 (tp30) cc_final: 0.7936 (tm-30) REVERT: A 1232 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7212 (mpp) REVERT: A 1234 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8230 (tm) REVERT: B 193 GLN cc_start: 0.7353 (mp10) cc_final: 0.6888 (mm-40) REVERT: B 269 ASP cc_start: 0.7633 (t70) cc_final: 0.7097 (t70) REVERT: B 374 LEU cc_start: 0.7091 (mt) cc_final: 0.6804 (mt) REVERT: B 418 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7001 (pmm) REVERT: B 462 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7942 (mp) REVERT: B 530 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8146 (mmp80) REVERT: B 722 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8574 (mtt) REVERT: B 1001 MET cc_start: 0.8831 (mmm) cc_final: 0.8178 (mtm) REVERT: B 1057 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6461 (tt0) REVERT: B 1061 ASP cc_start: 0.8207 (m-30) cc_final: 0.7812 (m-30) REVERT: B 1138 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8041 (mmt) REVERT: B 1142 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: B 1207 GLU cc_start: 0.8216 (tp30) cc_final: 0.7941 (tm-30) REVERT: B 1232 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7214 (mpp) REVERT: B 1234 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8208 (tm) REVERT: C 170 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8372 (OUTLIER) REVERT: C 193 GLN cc_start: 0.7395 (mp10) cc_final: 0.6926 (mm-40) REVERT: C 269 ASP cc_start: 0.7574 (t70) cc_final: 0.7057 (t70) REVERT: C 374 LEU cc_start: 0.7205 (mt) cc_final: 0.6914 (mt) REVERT: C 418 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7082 (pmm) REVERT: C 462 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7972 (mp) REVERT: C 722 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8571 (mtt) REVERT: C 1057 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6383 (tt0) REVERT: C 1061 ASP cc_start: 0.8256 (m-30) cc_final: 0.7865 (m-30) REVERT: C 1207 GLU cc_start: 0.8227 (tp30) cc_final: 0.7950 (tm-30) REVERT: C 1232 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7213 (mpp) REVERT: C 1234 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8261 (tm) REVERT: D 193 GLN cc_start: 0.7428 (mp10) cc_final: 0.6932 (mm-40) REVERT: D 269 ASP cc_start: 0.7629 (t70) cc_final: 0.7094 (t70) REVERT: D 287 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7894 (mp) REVERT: D 374 LEU cc_start: 0.7084 (mt) cc_final: 0.6773 (mt) REVERT: D 462 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7952 (mp) REVERT: D 530 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8160 (mmp80) REVERT: D 722 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8584 (mtt) REVERT: D 1057 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6398 (tt0) REVERT: D 1061 ASP cc_start: 0.8240 (m-30) cc_final: 0.7845 (m-30) REVERT: D 1138 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8123 (mmt) REVERT: D 1207 GLU cc_start: 0.8212 (tp30) cc_final: 0.7938 (tm-30) outliers start: 155 outliers final: 70 residues processed: 579 average time/residue: 0.5856 time to fit residues: 406.0983 Evaluate side-chains 583 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 480 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 ARG Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 530 ARG Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1057 GLU Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1142 GLU Chi-restraints excluded: chain B residue 1202 GLU Chi-restraints excluded: chain B residue 1232 MET Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 1007 MET Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1057 GLU Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 530 ARG Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1007 MET Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1057 GLU Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 311 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 269 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 314 GLN A 482 GLN A 586 HIS A 978 ASN A1035 ASN A1115 ASN B 171 HIS B 314 GLN B 482 GLN B 586 HIS B 978 ASN B1035 ASN B1115 ASN C 171 HIS C 314 GLN C 482 GLN C 586 HIS C 978 ASN C1035 ASN C1115 ASN D 171 HIS D 314 GLN D 586 HIS D 739 GLN D 978 ASN D1035 ASN D1115 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.172531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118472 restraints weight = 37187.397| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.41 r_work: 0.3214 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32968 Z= 0.122 Angle : 0.545 8.455 44584 Z= 0.267 Chirality : 0.038 0.133 4980 Planarity : 0.004 0.040 5516 Dihedral : 7.597 59.967 4528 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.87 % Allowed : 18.66 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.14), residues: 3824 helix: 1.88 (0.11), residues: 2424 sheet: 0.15 (0.36), residues: 204 loop : -1.92 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 354 TYR 0.016 0.001 TYR D 865 PHE 0.012 0.001 PHE D 162 TRP 0.012 0.001 TRP C 763 HIS 0.004 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (32968) covalent geometry : angle 0.54475 / 0.27 (44584) hydrogen bonds : bond 0.05331 / 3.61 ( 1735) hydrogen bonds : angle 3.51812 / 2.48 ( 5133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 503 time to evaluate : 1.011 Fit side-chains REVERT: A 263 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6412 (pp20) REVERT: A 264 ASP cc_start: 0.6109 (OUTLIER) cc_final: 0.5620 (m-30) REVERT: A 266 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6709 (mm) REVERT: A 269 ASP cc_start: 0.7351 (t70) cc_final: 0.6857 (t70) REVERT: A 374 LEU cc_start: 0.6421 (mt) cc_final: 0.6174 (mt) REVERT: A 418 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7022 (pmm) REVERT: A 722 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8166 (mtt) REVERT: A 963 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6753 (mp10) REVERT: A 1011 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.5498 (mmp) REVERT: A 1017 MET cc_start: 0.7732 (tmm) cc_final: 0.5649 (mtt) REVERT: A 1053 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8130 (ttm) REVERT: A 1138 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7699 (mmt) REVERT: A 1207 GLU cc_start: 0.7697 (tp30) cc_final: 0.7096 (tp30) REVERT: A 1234 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7516 (tm) REVERT: B 266 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6706 (mm) REVERT: B 269 ASP cc_start: 0.7325 (t70) cc_final: 0.6832 (t70) REVERT: B 374 LEU cc_start: 0.6433 (mt) cc_final: 0.6175 (mt) REVERT: B 722 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8169 (mtt) REVERT: B 1007 MET cc_start: 0.7644 (mtp) cc_final: 0.7329 (mtp) REVERT: B 1011 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.5537 (mmp) REVERT: B 1017 MET cc_start: 0.7729 (tmm) cc_final: 0.5647 (mtt) REVERT: B 1138 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7675 (mmt) REVERT: B 1207 GLU cc_start: 0.7681 (tp30) cc_final: 0.7075 (tp30) REVERT: B 1234 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7586 (tm) REVERT: C 170 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7749 (OUTLIER) REVERT: C 266 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6721 (mm) REVERT: C 269 ASP cc_start: 0.7330 (t70) cc_final: 0.6851 (t70) REVERT: C 374 LEU cc_start: 0.6394 (mt) cc_final: 0.6191 (mt) REVERT: C 525 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8078 (pp20) REVERT: C 722 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8172 (mtt) REVERT: C 1011 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.5537 (mmp) REVERT: C 1061 ASP cc_start: 0.8232 (m-30) cc_final: 0.7805 (m-30) REVERT: C 1138 MET cc_start: 0.8000 (mmt) cc_final: 0.7748 (mmm) REVERT: C 1207 GLU cc_start: 0.7662 (tp30) cc_final: 0.7073 (tp30) REVERT: C 1234 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7571 (tm) REVERT: D 266 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6633 (mm) REVERT: D 269 ASP cc_start: 0.7322 (t70) cc_final: 0.6830 (t70) REVERT: D 374 LEU cc_start: 0.6331 (mt) cc_final: 0.6091 (mt) REVERT: D 722 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8173 (mtt) REVERT: D 1011 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.5527 (mmp) REVERT: D 1207 GLU cc_start: 0.7689 (tp30) cc_final: 0.7085 (tp30) outliers start: 133 outliers final: 57 residues processed: 580 average time/residue: 0.5671 time to fit residues: 396.9043 Evaluate side-chains 537 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 457 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1199 GLN Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1199 GLN Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1199 GLN Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1185 ILE Chi-restraints excluded: chain D residue 1199 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 105 optimal weight: 7.9990 chunk 259 optimal weight: 0.9980 chunk 124 optimal weight: 0.0970 chunk 249 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 253 optimal weight: 0.0980 chunk 17 optimal weight: 10.0000 chunk 354 optimal weight: 1.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS A 978 ASN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS B 978 ASN ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS C 978 ASN ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 314 GLN D 586 HIS D 978 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.171394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116803 restraints weight = 36931.671| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.42 r_work: 0.3191 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32968 Z= 0.158 Angle : 0.565 7.756 44584 Z= 0.281 Chirality : 0.040 0.144 4980 Planarity : 0.004 0.062 5516 Dihedral : 7.571 59.245 4528 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.26 % Allowed : 19.74 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.14), residues: 3824 helix: 1.85 (0.11), residues: 2424 sheet: 0.17 (0.36), residues: 204 loop : -1.91 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 354 TYR 0.017 0.001 TYR B 865 PHE 0.015 0.001 PHE A 162 TRP 0.014 0.001 TRP A 763 HIS 0.006 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (32968) covalent geometry : angle 0.56504 / 0.28 (44584) hydrogen bonds : bond 0.05796 / 3.92 ( 1735) hydrogen bonds : angle 3.54030 / 2.49 ( 5133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 475 time to evaluate : 1.287 Fit side-chains REVERT: A 263 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6449 (pp20) REVERT: A 264 ASP cc_start: 0.6117 (OUTLIER) cc_final: 0.5648 (m-30) REVERT: A 266 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6464 (mm) REVERT: A 269 ASP cc_start: 0.7346 (t70) cc_final: 0.6852 (t70) REVERT: A 374 LEU cc_start: 0.6464 (mt) cc_final: 0.6227 (mt) REVERT: A 418 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7014 (pmm) REVERT: A 482 GLN cc_start: 0.6900 (mp10) cc_final: 0.6496 (tm130) REVERT: A 722 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8219 (mtt) REVERT: A 963 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6815 (mp10) REVERT: A 1011 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.5494 (mmp) REVERT: A 1017 MET cc_start: 0.7742 (tmm) cc_final: 0.5688 (mtt) REVERT: A 1053 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8165 (ttm) REVERT: A 1138 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7710 (mmt) REVERT: A 1207 GLU cc_start: 0.7716 (tp30) cc_final: 0.7116 (tp30) REVERT: A 1234 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7539 (tm) REVERT: B 266 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6714 (mm) REVERT: B 269 ASP cc_start: 0.7348 (t70) cc_final: 0.6848 (t70) REVERT: B 374 LEU cc_start: 0.6461 (mt) cc_final: 0.6213 (mt) REVERT: B 418 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7290 (pmt) REVERT: B 482 GLN cc_start: 0.6734 (mp10) cc_final: 0.6397 (tm130) REVERT: B 525 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7760 (pp20) REVERT: B 722 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8212 (mtt) REVERT: B 1011 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.5678 (mmp) REVERT: B 1138 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7743 (mmt) REVERT: B 1207 GLU cc_start: 0.7714 (tp30) cc_final: 0.7108 (tp30) REVERT: B 1234 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7608 (tm) REVERT: C 170 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7766 (OUTLIER) REVERT: C 266 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6731 (mm) REVERT: C 269 ASP cc_start: 0.7355 (t70) cc_final: 0.6858 (t70) REVERT: C 374 LEU cc_start: 0.6453 (mt) cc_final: 0.6208 (mt) REVERT: C 418 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7304 (pmt) REVERT: C 482 GLN cc_start: 0.6697 (mp10) cc_final: 0.6392 (tm130) REVERT: C 525 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8082 (pp20) REVERT: C 722 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8220 (mtt) REVERT: C 1001 MET cc_start: 0.8232 (mtt) cc_final: 0.7810 (mtm) REVERT: C 1011 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.5508 (mmp) REVERT: C 1017 MET cc_start: 0.7738 (tmm) cc_final: 0.5691 (mtt) REVERT: C 1138 MET cc_start: 0.8003 (mmt) cc_final: 0.7744 (mmm) REVERT: C 1207 GLU cc_start: 0.7723 (tp30) cc_final: 0.7116 (tp30) REVERT: C 1234 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7634 (tm) REVERT: D 263 GLU cc_start: 0.7469 (mp0) cc_final: 0.7154 (mp0) REVERT: D 266 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6633 (mm) REVERT: D 269 ASP cc_start: 0.7341 (t70) cc_final: 0.6843 (t70) REVERT: D 287 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7279 (mp) REVERT: D 374 LEU cc_start: 0.6347 (mt) cc_final: 0.6097 (mt) REVERT: D 482 GLN cc_start: 0.6863 (mp10) cc_final: 0.6447 (tm130) REVERT: D 722 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8210 (mtt) REVERT: D 1011 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.5510 (mmp) REVERT: D 1142 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: D 1207 GLU cc_start: 0.7721 (tp30) cc_final: 0.7117 (tp30) outliers start: 112 outliers final: 52 residues processed: 542 average time/residue: 0.5674 time to fit residues: 370.6921 Evaluate side-chains 547 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 467 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1142 GLU Chi-restraints excluded: chain D residue 1185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 60 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 358 optimal weight: 7.9990 chunk 356 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 314 GLN A 586 HIS A 978 ASN A1035 ASN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS B 978 ASN B1035 ASN ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 314 GLN C 586 HIS C 978 ASN C1035 ASN ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 314 GLN D 586 HIS D 978 ASN D1035 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.172543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117955 restraints weight = 37281.564| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.43 r_work: 0.3208 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32968 Z= 0.135 Angle : 0.555 7.917 44584 Z= 0.274 Chirality : 0.039 0.138 4980 Planarity : 0.004 0.071 5516 Dihedral : 7.449 58.505 4528 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.09 % Allowed : 19.83 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.14), residues: 3824 helix: 1.96 (0.11), residues: 2424 sheet: 0.22 (0.36), residues: 204 loop : -1.86 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 354 TYR 0.018 0.001 TYR B 865 PHE 0.014 0.001 PHE D 162 TRP 0.013 0.001 TRP A 763 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (32968) covalent geometry : angle 0.55507 / 0.27 (44584) hydrogen bonds : bond 0.05421 / 3.67 ( 1735) hydrogen bonds : angle 3.49904 / 2.47 ( 5133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 472 time to evaluate : 1.188 Fit side-chains REVERT: A 263 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6762 (pp20) REVERT: A 269 ASP cc_start: 0.7331 (t70) cc_final: 0.6832 (t70) REVERT: A 374 LEU cc_start: 0.6465 (mt) cc_final: 0.6232 (mt) REVERT: A 418 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6917 (pmm) REVERT: A 482 GLN cc_start: 0.6857 (mp10) cc_final: 0.6449 (tm130) REVERT: A 525 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7726 (pp20) REVERT: A 722 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8173 (mtt) REVERT: A 963 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.6735 (mp10) REVERT: A 1011 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.5490 (mmp) REVERT: A 1017 MET cc_start: 0.7796 (tmm) cc_final: 0.5738 (mtt) REVERT: A 1053 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8101 (ttm) REVERT: A 1138 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7744 (mmt) REVERT: A 1207 GLU cc_start: 0.7705 (tp30) cc_final: 0.7112 (tp30) REVERT: B 263 GLU cc_start: 0.7461 (mp0) cc_final: 0.7158 (mp0) REVERT: B 266 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6650 (mm) REVERT: B 269 ASP cc_start: 0.7338 (t70) cc_final: 0.6835 (t70) REVERT: B 374 LEU cc_start: 0.6448 (mt) cc_final: 0.6204 (mt) REVERT: B 482 GLN cc_start: 0.6665 (mp10) cc_final: 0.6328 (tm130) REVERT: B 525 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7689 (pp20) REVERT: B 722 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8174 (mtt) REVERT: B 1007 MET cc_start: 0.7637 (mtp) cc_final: 0.7329 (mtp) REVERT: B 1011 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.5618 (mmp) REVERT: B 1138 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7797 (mmt) REVERT: B 1207 GLU cc_start: 0.7712 (tp30) cc_final: 0.7116 (tp30) REVERT: B 1234 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7586 (tm) REVERT: C 170 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7758 (OUTLIER) REVERT: C 263 GLU cc_start: 0.7414 (mp0) cc_final: 0.7143 (mp0) REVERT: C 269 ASP cc_start: 0.7346 (t70) cc_final: 0.6848 (t70) REVERT: C 374 LEU cc_start: 0.6442 (mt) cc_final: 0.6202 (mt) REVERT: C 482 GLN cc_start: 0.6658 (mp10) cc_final: 0.6328 (tm130) REVERT: C 525 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8083 (pp20) REVERT: C 722 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8183 (mtt) REVERT: C 1001 MET cc_start: 0.8061 (mtt) cc_final: 0.7614 (mtm) REVERT: C 1011 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.5517 (mmp) REVERT: C 1138 MET cc_start: 0.7998 (mmt) cc_final: 0.7743 (mmm) REVERT: C 1207 GLU cc_start: 0.7720 (tp30) cc_final: 0.7119 (tp30) REVERT: C 1234 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7613 (tm) REVERT: D 263 GLU cc_start: 0.7422 (mp0) cc_final: 0.7134 (mp0) REVERT: D 269 ASP cc_start: 0.7334 (t70) cc_final: 0.6828 (t70) REVERT: D 374 LEU cc_start: 0.6335 (mt) cc_final: 0.6090 (mt) REVERT: D 482 GLN cc_start: 0.6813 (mp10) cc_final: 0.6465 (tm130) REVERT: D 525 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7767 (pp20) REVERT: D 722 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8180 (mtt) REVERT: D 1001 MET cc_start: 0.8051 (mtt) cc_final: 0.7631 (mtm) REVERT: D 1011 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.5519 (mmp) REVERT: D 1142 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: D 1207 GLU cc_start: 0.7716 (tp30) cc_final: 0.7118 (tp30) REVERT: D 1232 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6981 (mpp) outliers start: 106 outliers final: 48 residues processed: 528 average time/residue: 0.5462 time to fit residues: 346.7347 Evaluate side-chains 535 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 464 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1234 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1142 GLU Chi-restraints excluded: chain D residue 1185 ILE Chi-restraints excluded: chain D residue 1232 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 49 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS A 978 ASN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS B 978 ASN ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS C 978 ASN ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 HIS D 978 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.171189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116513 restraints weight = 37132.897| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.41 r_work: 0.3190 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32968 Z= 0.165 Angle : 0.581 9.095 44584 Z= 0.288 Chirality : 0.040 0.147 4980 Planarity : 0.004 0.073 5516 Dihedral : 7.448 58.045 4528 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.91 % Allowed : 20.06 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.14), residues: 3824 helix: 1.89 (0.11), residues: 2424 sheet: 0.19 (0.36), residues: 204 loop : -1.91 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 354 TYR 0.018 0.001 TYR D 865 PHE 0.016 0.001 PHE A 162 TRP 0.014 0.001 TRP A 763 HIS 0.005 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (32968) covalent geometry : angle 0.58060 / 0.29 (44584) hydrogen bonds : bond 0.05955 / 4.02 ( 1735) hydrogen bonds : angle 3.55202 / 2.50 ( 5133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11775.92 seconds wall clock time: 200 minutes 58.50 seconds (12058.50 seconds total)