Starting phenix.real_space_refine on Sat Mar 7 13:02:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7crc_30450/03_2026/7crc_30450.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crc_30450/03_2026/7crc_30450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7crc_30450/03_2026/7crc_30450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crc_30450/03_2026/7crc_30450.map" model { file = "/net/cci-nas-00/data/ceres_data/7crc_30450/03_2026/7crc_30450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crc_30450/03_2026/7crc_30450.cif" } resolution = 3.02 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 248 5.16 5 C 27437 2.51 5 N 7397 2.21 5 O 8072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43168 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8850 Classifications: {'peptide': 1108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 41, 'TRANS': 1066} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 8886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8886 Classifications: {'peptide': 1112} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 41, 'TRANS': 1070} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 8844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8844 Classifications: {'peptide': 1108} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 41, 'TRANS': 1066} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1883 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1911 Chain: "H" Number of atoms: 1883 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1911 Chain: "F" Number of atoms: 1883 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1911 Chain: "G" Number of atoms: 1883 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1911 Chain: "D" Number of atoms: 8886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8886 Classifications: {'peptide': 1112} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 41, 'TRANS': 1070} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.24, per 1000 atoms: 0.26 Number of scatterers: 43168 At special positions: 0 Unit cell: (216.286, 218.482, 141.629, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 248 16.00 P 14 15.00 O 8072 8.00 N 7397 7.00 C 27437 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: 3.56 Conformation dependent library (CDL) restraints added in 2.4 seconds 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10288 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 23 sheets defined 43.6% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.613A pdb=" N ARG A 123 " --> pdb=" O ASN A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 Processing helix chain 'A' and resid 148 through 151 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 181 through 188 Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.617A pdb=" N LYS A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 221 removed outlier: 3.554A pdb=" N ILE A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.184A pdb=" N ARG A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 231 through 248 Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.936A pdb=" N HIS A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 272 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 278 Processing helix chain 'A' and resid 292 through 305 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 327 through 345 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.891A pdb=" N LEU A 379 " --> pdb=" O GLN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.557A pdb=" N PHE A 389 " --> pdb=" O THR A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 408 removed outlier: 4.099A pdb=" N LEU A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 444 through 453 removed outlier: 3.846A pdb=" N GLU A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 467 Processing helix chain 'A' and resid 471 through 485 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 487 through 500 removed outlier: 3.842A pdb=" N ILE A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 515 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 533 through 544 Processing helix chain 'A' and resid 557 through 571 removed outlier: 3.861A pdb=" N ARG A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.948A pdb=" N VAL A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 643 through 652 removed outlier: 3.519A pdb=" N GLN A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 745 removed outlier: 3.621A pdb=" N ILE A 742 " --> pdb=" O PRO A 739 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 743 " --> pdb=" O SER A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 838 Processing helix chain 'A' and resid 856 through 862 removed outlier: 3.530A pdb=" N ILE A 859 " --> pdb=" O PRO A 856 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY A 860 " --> pdb=" O SER A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 886 removed outlier: 3.530A pdb=" N ILE A 883 " --> pdb=" O PRO A 880 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A 884 " --> pdb=" O SER A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 953 removed outlier: 3.880A pdb=" N MET A 951 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 removed outlier: 3.544A pdb=" N LEU A 967 " --> pdb=" O PHE A 964 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 968 " --> pdb=" O GLU A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 964 through 968' Processing helix chain 'A' and resid 970 through 975 removed outlier: 3.619A pdb=" N LEU A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 975' Processing helix chain 'A' and resid 990 through 995 Processing helix chain 'A' and resid 1054 through 1064 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 99 through 110 removed outlier: 4.267A pdb=" N HIS B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'B' and resid 152 through 169 Processing helix chain 'B' and resid 181 through 188 removed outlier: 3.575A pdb=" N ILE B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 204 through 220 removed outlier: 3.622A pdb=" N VAL B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 231 through 247 removed outlier: 3.574A pdb=" N MET B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.649A pdb=" N GLN B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 272 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 305 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 316 through 321 removed outlier: 3.569A pdb=" N CYS B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 344 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.940A pdb=" N LEU B 379 " --> pdb=" O GLN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 401 through 408 removed outlier: 3.988A pdb=" N LEU B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 456 through 467 Processing helix chain 'B' and resid 471 through 485 Proline residue: B 480 - end of helix Processing helix chain 'B' and resid 487 through 500 removed outlier: 3.640A pdb=" N ILE B 493 " --> pdb=" O LYS B 489 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 515 Processing helix chain 'B' and resid 520 through 529 Processing helix chain 'B' and resid 533 through 544 Processing helix chain 'B' and resid 557 through 571 removed outlier: 4.224A pdb=" N ARG B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 595 Processing helix chain 'B' and resid 599 through 601 No H-bonds generated for 'chain 'B' and resid 599 through 601' Processing helix chain 'B' and resid 620 through 626 removed outlier: 3.504A pdb=" N GLU B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 651 Processing helix chain 'B' and resid 739 through 745 Processing helix chain 'B' and resid 832 through 838 Processing helix chain 'B' and resid 856 through 862 removed outlier: 4.078A pdb=" N GLY B 860 " --> pdb=" O SER B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 886 removed outlier: 3.785A pdb=" N GLY B 884 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 953 removed outlier: 4.099A pdb=" N ILE B 950 " --> pdb=" O PRO B 947 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET B 951 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 968 removed outlier: 3.921A pdb=" N LEU B 967 " --> pdb=" O PHE B 964 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS B 968 " --> pdb=" O GLU B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 964 through 968' Processing helix chain 'B' and resid 970 through 975 removed outlier: 3.771A pdb=" N ASP B 975 " --> pdb=" O PRO B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 995 removed outlier: 3.704A pdb=" N VAL B 993 " --> pdb=" O PRO B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1063 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 119 through 123 removed outlier: 3.709A pdb=" N ARG C 123 " --> pdb=" O ASN C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 removed outlier: 3.515A pdb=" N LYS C 132 " --> pdb=" O GLY C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 151 Processing helix chain 'C' and resid 152 through 169 Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 204 through 221 Processing helix chain 'C' and resid 231 through 246 Processing helix chain 'C' and resid 261 through 274 removed outlier: 3.886A pdb=" N HIS C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU C 272 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 278 removed outlier: 3.593A pdb=" N ASP C 278 " --> pdb=" O LEU C 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 275 through 278' Processing helix chain 'C' and resid 292 through 305 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 327 through 345 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.886A pdb=" N LEU C 379 " --> pdb=" O GLN C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 401 through 409 removed outlier: 4.153A pdb=" N LEU C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.729A pdb=" N GLU C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 468 Processing helix chain 'C' and resid 471 through 485 Proline residue: C 480 - end of helix Processing helix chain 'C' and resid 487 through 500 removed outlier: 3.755A pdb=" N ILE C 493 " --> pdb=" O LYS C 489 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 500 " --> pdb=" O PHE C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 515 Processing helix chain 'C' and resid 520 through 533 removed outlier: 5.601A pdb=" N LYS C 530 " --> pdb=" O GLY C 526 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP C 533 " --> pdb=" O GLY C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 544 Processing helix chain 'C' and resid 557 through 568 Processing helix chain 'C' and resid 589 through 594 Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 644 through 652 removed outlier: 3.668A pdb=" N GLN C 652 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 745 removed outlier: 3.833A pdb=" N GLU C 743 " --> pdb=" O SER C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 838 Processing helix chain 'C' and resid 856 through 862 removed outlier: 3.515A pdb=" N ILE C 859 " --> pdb=" O PRO C 856 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY C 860 " --> pdb=" O SER C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 886 removed outlier: 3.599A pdb=" N ILE C 883 " --> pdb=" O PRO C 880 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY C 884 " --> pdb=" O SER C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 953 removed outlier: 3.897A pdb=" N MET C 951 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 968 removed outlier: 3.973A pdb=" N LYS C 968 " --> pdb=" O GLU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 975 removed outlier: 3.583A pdb=" N LEU C 974 " --> pdb=" O PHE C 970 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP C 975 " --> pdb=" O PRO C 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 970 through 975' Processing helix chain 'C' and resid 990 through 995 removed outlier: 3.542A pdb=" N VAL C 993 " --> pdb=" O PRO C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1064 Processing helix chain 'E' and resid 68 through 84 removed outlier: 3.982A pdb=" N SER E 84 " --> pdb=" O HIS E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 102 removed outlier: 5.084A pdb=" N VAL E 95 " --> pdb=" O MET E 91 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG E 96 " --> pdb=" O LYS E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 118 Processing helix chain 'E' and resid 125 through 138 removed outlier: 3.536A pdb=" N ALA E 129 " --> pdb=" O THR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 150 removed outlier: 4.023A pdb=" N ARG E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 177 Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 198 through 210 removed outlier: 4.475A pdb=" N PHE E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 223 Processing helix chain 'E' and resid 226 through 238 Processing helix chain 'E' and resid 244 through 261 removed outlier: 3.904A pdb=" N PHE E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS E 258 " --> pdb=" O TRP E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 278 removed outlier: 3.505A pdb=" N SER E 278 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 310 removed outlier: 4.041A pdb=" N ARG E 308 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR E 310 " --> pdb=" O TYR E 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 84 removed outlier: 3.936A pdb=" N SER H 84 " --> pdb=" O HIS H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 102 removed outlier: 4.573A pdb=" N VAL H 95 " --> pdb=" O MET H 91 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG H 96 " --> pdb=" O LYS H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 118 Processing helix chain 'H' and resid 125 through 138 Processing helix chain 'H' and resid 139 through 149 Processing helix chain 'H' and resid 157 through 177 Processing helix chain 'H' and resid 180 through 189 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 198 through 210 removed outlier: 4.341A pdb=" N PHE H 204 " --> pdb=" O THR H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 223 Processing helix chain 'H' and resid 226 through 238 Processing helix chain 'H' and resid 244 through 261 Processing helix chain 'H' and resid 265 through 277 removed outlier: 3.926A pdb=" N TYR H 276 " --> pdb=" O THR H 272 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN H 277 " --> pdb=" O LEU H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 310 removed outlier: 4.058A pdb=" N ARG H 308 " --> pdb=" O GLU H 304 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE H 309 " --> pdb=" O GLU H 305 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR H 310 " --> pdb=" O TYR H 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 84 removed outlier: 3.923A pdb=" N SER F 84 " --> pdb=" O HIS F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 removed outlier: 4.586A pdb=" N VAL F 95 " --> pdb=" O MET F 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG F 96 " --> pdb=" O LYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 118 Processing helix chain 'F' and resid 125 through 138 Processing helix chain 'F' and resid 139 through 150 Processing helix chain 'F' and resid 157 through 177 Processing helix chain 'F' and resid 180 through 189 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 198 through 210 removed outlier: 4.345A pdb=" N PHE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 223 Processing helix chain 'F' and resid 226 through 238 Processing helix chain 'F' and resid 244 through 261 Processing helix chain 'F' and resid 265 through 277 removed outlier: 4.194A pdb=" N TYR F 276 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 310 removed outlier: 4.062A pdb=" N ARG F 308 " --> pdb=" O GLU F 304 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR F 310 " --> pdb=" O TYR F 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 84 removed outlier: 3.888A pdb=" N SER G 84 " --> pdb=" O HIS G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 102 removed outlier: 4.906A pdb=" N VAL G 95 " --> pdb=" O MET G 91 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 118 Processing helix chain 'G' and resid 125 through 138 Processing helix chain 'G' and resid 139 through 150 removed outlier: 3.637A pdb=" N ARG G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 177 Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 198 through 210 removed outlier: 4.403A pdb=" N PHE G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 223 Processing helix chain 'G' and resid 226 through 238 Processing helix chain 'G' and resid 244 through 261 removed outlier: 3.872A pdb=" N PHE G 256 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS G 258 " --> pdb=" O TRP G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 278 removed outlier: 3.903A pdb=" N TYR G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER G 278 " --> pdb=" O ALA G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 310 removed outlier: 4.120A pdb=" N ARG G 308 " --> pdb=" O GLU G 304 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE G 309 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR G 310 " --> pdb=" O TYR G 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 99 through 110 removed outlier: 4.253A pdb=" N HIS D 103 " --> pdb=" O THR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 126 through 137 removed outlier: 3.637A pdb=" N LYS D 132 " --> pdb=" O GLY D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 151 Processing helix chain 'D' and resid 152 through 170 Processing helix chain 'D' and resid 181 through 188 removed outlier: 3.558A pdb=" N ILE D 185 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 200 removed outlier: 3.613A pdb=" N PHE D 196 " --> pdb=" O PHE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.576A pdb=" N VAL D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 231 through 247 Processing helix chain 'D' and resid 261 through 274 removed outlier: 4.353A pdb=" N HIS D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 272 " --> pdb=" O MET D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 316 through 321 removed outlier: 3.670A pdb=" N CYS D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 344 removed outlier: 3.510A pdb=" N MET D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 361 Processing helix chain 'D' and resid 375 through 383 removed outlier: 4.116A pdb=" N LEU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 401 through 408 removed outlier: 4.105A pdb=" N LEU D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 433 Processing helix chain 'D' and resid 442 through 454 removed outlier: 3.602A pdb=" N LEU D 452 " --> pdb=" O GLU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 485 Proline residue: D 480 - end of helix Processing helix chain 'D' and resid 487 through 500 removed outlier: 3.767A pdb=" N ILE D 493 " --> pdb=" O LYS D 489 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 497 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D 500 " --> pdb=" O PHE D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 515 Processing helix chain 'D' and resid 520 through 528 Processing helix chain 'D' and resid 533 through 544 Processing helix chain 'D' and resid 557 through 571 removed outlier: 3.540A pdb=" N GLY D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG D 569 " --> pdb=" O ARG D 565 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 626 removed outlier: 4.270A pdb=" N ARG D 626 " --> pdb=" O LYS D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 739 through 745 removed outlier: 3.722A pdb=" N GLU D 743 " --> pdb=" O SER D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 832 through 838 Processing helix chain 'D' and resid 856 through 862 removed outlier: 4.129A pdb=" N GLY D 860 " --> pdb=" O SER D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 886 removed outlier: 3.558A pdb=" N ILE D 883 " --> pdb=" O PRO D 880 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY D 884 " --> pdb=" O SER D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 953 removed outlier: 4.010A pdb=" N ILE D 950 " --> pdb=" O PRO D 947 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET D 951 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 975 removed outlier: 3.580A pdb=" N LEU D 974 " --> pdb=" O PHE D 970 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP D 975 " --> pdb=" O PRO D 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 970 through 975' Processing helix chain 'D' and resid 1054 through 1064 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 314 removed outlier: 6.292A pdb=" N VAL A 366 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE A 396 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 368 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR A 398 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A 370 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 283 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR A 399 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 285 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N TYR A 414 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY A 284 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574 removed outlier: 5.960A pdb=" N PHE A 603 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN A 581 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY A 605 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU A 659 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N MET A 704 " --> pdb=" O LYS A 728 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 821 " --> pdb=" O LEU A 797 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 843 through 845 removed outlier: 6.874A pdb=" N LEU A 844 " --> pdb=" O TYR A 869 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N SER A 871 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 868 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 892 " --> pdb=" O THR A 914 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 918 " --> pdb=" O MET A 894 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 939 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 961 " --> pdb=" O GLU A 979 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 981 " --> pdb=" O ILE A 961 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1022 through 1024 removed outlier: 6.251A pdb=" N LEU A1023 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU A1045 " --> pdb=" O MET A1071 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A1189 " --> pdb=" O MET A1111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1093 through 1094 Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 90 removed outlier: 6.240A pdb=" N GLN B 86 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE B 142 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 88 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU B 144 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER B 90 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 310 through 314 removed outlier: 6.643A pdb=" N LEU B 310 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL B 369 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 312 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASP B 371 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET B 314 " --> pdb=" O ASP B 371 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 283 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR B 399 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 285 " --> pdb=" O THR B 399 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR B 414 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY B 284 " --> pdb=" O TYR B 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 548 through 549 Processing sheet with id=AB1, first strand: chain 'B' and resid 581 through 585 removed outlier: 7.533A pdb=" N GLN B 581 " --> pdb=" O GLY B 605 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ASN B 607 " --> pdb=" O GLN B 581 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 583 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASP B 609 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY B 585 " --> pdb=" O ASP B 609 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 604 " --> pdb=" O PHE B 632 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ARG B 634 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE B 606 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASN B 636 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU B 608 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 659 " --> pdb=" O ASP B 682 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET B 704 " --> pdb=" O LYS B 728 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG B 730 " --> pdb=" O MET B 704 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 706 " --> pdb=" O ARG B 730 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 751 " --> pdb=" O ASN B 775 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU B 774 " --> pdb=" O SER B 798 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN B 821 " --> pdb=" O LEU B 797 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 843 through 845 removed outlier: 7.044A pdb=" N LEU B 844 " --> pdb=" O TYR B 869 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N SER B 871 " --> pdb=" O LEU B 844 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 892 " --> pdb=" O THR B 914 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 918 " --> pdb=" O MET B 894 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 939 " --> pdb=" O LEU B 917 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 961 " --> pdb=" O GLU B 979 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 981 " --> pdb=" O ILE B 961 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 980 " --> pdb=" O ARG B1003 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B1023 " --> pdb=" O TYR B1046 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU B1045 " --> pdb=" O MET B1071 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS B1157 " --> pdb=" O LEU B1112 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B1112 " --> pdb=" O HIS B1157 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B1189 " --> pdb=" O MET B1111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1093 through 1095 Processing sheet with id=AB4, first strand: chain 'C' and resid 88 through 90 Processing sheet with id=AB5, first strand: chain 'C' and resid 310 through 314 removed outlier: 6.427A pdb=" N ILE C 283 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR C 399 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE C 285 " --> pdb=" O THR C 399 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR C 414 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY C 284 " --> pdb=" O TYR C 414 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 573 through 574 removed outlier: 5.753A pdb=" N PHE C 603 " --> pdb=" O LYS C 579 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN C 581 " --> pdb=" O PHE C 603 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY C 605 " --> pdb=" O GLN C 581 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 604 " --> pdb=" O PHE C 632 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ARG C 634 " --> pdb=" O ILE C 604 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE C 606 " --> pdb=" O ARG C 634 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASN C 636 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU C 608 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU C 659 " --> pdb=" O ASP C 682 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU C 681 " --> pdb=" O ASP C 705 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N MET C 704 " --> pdb=" O LYS C 728 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 821 " --> pdb=" O LEU C 797 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 843 through 845 removed outlier: 7.015A pdb=" N LEU C 844 " --> pdb=" O TYR C 869 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N SER C 871 " --> pdb=" O LEU C 844 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 892 " --> pdb=" O THR C 914 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 918 " --> pdb=" O MET C 894 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 939 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE C 961 " --> pdb=" O GLU C 979 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU C 980 " --> pdb=" O ARG C1003 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG C1000 " --> pdb=" O TYR C1022 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N TYR C1024 " --> pdb=" O ARG C1000 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C1002 " --> pdb=" O TYR C1024 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C1045 " --> pdb=" O MET C1071 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N HIS C1157 " --> pdb=" O LEU C1112 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU C1112 " --> pdb=" O HIS C1157 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU C1189 " --> pdb=" O MET C1111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1093 through 1095 removed outlier: 3.657A pdb=" N LEU C1173 " --> pdb=" O LEU C1095 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 85 through 90 removed outlier: 6.290A pdb=" N GLN D 86 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE D 142 " --> pdb=" O GLN D 86 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE D 88 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU D 144 " --> pdb=" O PHE D 88 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER D 90 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS D 139 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET D 174 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA D 141 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE D 176 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL D 143 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 310 through 314 removed outlier: 6.379A pdb=" N ILE D 283 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR D 399 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE D 285 " --> pdb=" O THR D 399 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR D 414 " --> pdb=" O MET D 282 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY D 284 " --> pdb=" O TYR D 414 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 548 through 549 Processing sheet with id=AC3, first strand: chain 'D' and resid 581 through 585 removed outlier: 7.482A pdb=" N GLN D 581 " --> pdb=" O GLY D 605 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N ASN D 607 " --> pdb=" O GLN D 581 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 583 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASP D 609 " --> pdb=" O LEU D 583 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLY D 585 " --> pdb=" O ASP D 609 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE D 604 " --> pdb=" O PHE D 632 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ARG D 634 " --> pdb=" O ILE D 604 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE D 606 " --> pdb=" O ARG D 634 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASN D 636 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU D 608 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL D 633 " --> pdb=" O HIS D 660 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LYS D 662 " --> pdb=" O VAL D 633 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE D 635 " --> pdb=" O LYS D 662 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET D 704 " --> pdb=" O LYS D 728 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU D 774 " --> pdb=" O SER D 798 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU D 797 " --> pdb=" O ASN D 821 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 843 through 845 removed outlier: 7.050A pdb=" N LEU D 844 " --> pdb=" O TYR D 869 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N SER D 871 " --> pdb=" O LEU D 844 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 892 " --> pdb=" O THR D 914 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE D 918 " --> pdb=" O MET D 894 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 939 " --> pdb=" O LEU D 917 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE D 961 " --> pdb=" O GLU D 979 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU D1023 " --> pdb=" O TYR D1046 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU D1045 " --> pdb=" O MET D1071 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N HIS D1157 " --> pdb=" O LEU D1112 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU D1112 " --> pdb=" O HIS D1157 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU D1189 " --> pdb=" O MET D1111 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D1085 " --> pdb=" O CYS D1190 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS D1083 " --> pdb=" O ILE D1192 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1093 through 1096 removed outlier: 3.621A pdb=" N LEU D1173 " --> pdb=" O LEU D1095 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER D1125 " --> pdb=" O VAL D1180 " (cutoff:3.500A) 1697 hydrogen bonds defined for protein. 4676 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: 10.75 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7155 1.32 - 1.44: 11310 1.44 - 1.56: 25181 1.56 - 1.69: 22 1.69 - 1.81: 364 Bond restraints: 44032 Sorted by residual: bond pdb=" C4 ATP B1302 " pdb=" C5 ATP B1302 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.22e+01 bond pdb=" C4 ATP D1302 " pdb=" C5 ATP D1302 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.21e+01 bond pdb=" C5 ATP D1302 " pdb=" C6 ATP D1302 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.90e+01 bond pdb=" C5 ATP B1302 " pdb=" C6 ATP B1302 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.70e+01 bond pdb=" C8 ATP D1302 " pdb=" N7 ATP D1302 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.20e+01 ... (remaining 44027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 59032 3.49 - 6.99: 458 6.99 - 10.48: 43 10.48 - 13.98: 0 13.98 - 17.47: 4 Bond angle restraints: 59537 Sorted by residual: angle pdb=" PB ATP D1302 " pdb=" O3B ATP D1302 " pdb=" PG ATP D1302 " ideal model delta sigma weight residual 139.87 122.40 17.47 1.00e+00 1.00e+00 3.05e+02 angle pdb=" PB ATP B1302 " pdb=" O3B ATP B1302 " pdb=" PG ATP B1302 " ideal model delta sigma weight residual 139.87 122.63 17.24 1.00e+00 1.00e+00 2.97e+02 angle pdb=" PA ATP D1302 " pdb=" O3A ATP D1302 " pdb=" PB ATP D1302 " ideal model delta sigma weight residual 136.83 121.54 15.29 1.00e+00 1.00e+00 2.34e+02 angle pdb=" PA ATP B1302 " pdb=" O3A ATP B1302 " pdb=" PB ATP B1302 " ideal model delta sigma weight residual 136.83 121.61 15.22 1.00e+00 1.00e+00 2.32e+02 angle pdb=" N ASP B1026 " pdb=" CA ASP B1026 " pdb=" C ASP B1026 " ideal model delta sigma weight residual 111.07 120.16 -9.09 1.07e+00 8.73e-01 7.22e+01 ... (remaining 59532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.19: 25116 20.19 - 40.37: 1511 40.37 - 60.56: 169 60.56 - 80.74: 39 80.74 - 100.93: 16 Dihedral angle restraints: 26851 sinusoidal: 11023 harmonic: 15828 Sorted by residual: dihedral pdb=" C ASP C 278 " pdb=" N ASP C 278 " pdb=" CA ASP C 278 " pdb=" CB ASP C 278 " ideal model delta harmonic sigma weight residual -122.60 -136.86 14.26 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" O1B ADP C1301 " pdb=" O3A ADP C1301 " pdb=" PB ADP C1301 " pdb=" PA ADP C1301 " ideal model delta sinusoidal sigma weight residual -60.00 40.93 -100.93 1 2.00e+01 2.50e-03 2.86e+01 dihedral pdb=" CA LEU B 923 " pdb=" C LEU B 923 " pdb=" N LYS B 924 " pdb=" CA LYS B 924 " ideal model delta harmonic sigma weight residual 180.00 153.42 26.58 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 26848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 6187 0.089 - 0.178: 499 0.178 - 0.267: 55 0.267 - 0.356: 10 0.356 - 0.446: 3 Chirality restraints: 6754 Sorted by residual: chirality pdb=" CA ASP C 278 " pdb=" N ASP C 278 " pdb=" C ASP C 278 " pdb=" CB ASP C 278 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA LEU D 753 " pdb=" N LEU D 753 " pdb=" C LEU D 753 " pdb=" CB LEU D 753 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CA LEU D1034 " pdb=" N LEU D1034 " pdb=" C LEU D1034 " pdb=" CB LEU D1034 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 6751 not shown) Planarity restraints: 7543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B1033 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C ARG B1033 " -0.068 2.00e-02 2.50e+03 pdb=" O ARG B1033 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU B1034 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B1034 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C LEU B1034 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU B1034 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP B1035 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 138 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C TYR H 138 " -0.055 2.00e-02 2.50e+03 pdb=" O TYR H 138 " 0.020 2.00e-02 2.50e+03 pdb=" N SER H 139 " 0.019 2.00e-02 2.50e+03 ... (remaining 7540 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1838 2.71 - 3.26: 45038 3.26 - 3.81: 68939 3.81 - 4.35: 87098 4.35 - 4.90: 143781 Nonbonded interactions: 346694 Sorted by model distance: nonbonded pdb=" OG1 THR C1155 " pdb=" OE1 GLU C1156 " model vdw 2.167 3.040 nonbonded pdb=" O SER D 949 " pdb=" OG SER D 952 " model vdw 2.198 3.040 nonbonded pdb=" O ASP A 217 " pdb=" OG1 THR A 220 " model vdw 2.213 3.040 nonbonded pdb=" O LEU C1060 " pdb=" OG1 THR C1064 " model vdw 2.217 3.040 nonbonded pdb=" O LEU A1060 " pdb=" OG1 THR A1064 " model vdw 2.219 3.040 ... (remaining 346689 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 85 through 386 or (resid 387 and (name N or name CA or nam \ e C or name O or name CB )) or resid 388 through 598 or (resid 599 and (name N o \ r name CA or name C or name O or name CB )) or resid 600 through 1301)) selection = (chain 'B' and (resid 85 through 386 or (resid 387 and (name N or name CA or nam \ e C or name O or name CB )) or resid 388 through 1038 or (resid 1039 through 104 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 1043 through \ 1301)) selection = (chain 'C' and (resid 85 through 598 or (resid 599 and (name N or name CA or nam \ e C or name O or name CB )) or resid 600 through 1301)) selection = (chain 'D' and (resid 85 through 386 or (resid 387 and (name N or name CA or nam \ e C or name O or name CB )) or resid 388 through 1038 or (resid 1039 through 104 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 1043 through \ 1301)) } ncs_group { reference = (chain 'E' and (resid 67 through 78 or resid 80 through 311)) selection = (chain 'F' and (resid 67 through 78 or resid 80 through 311)) selection = (chain 'G' and (resid 67 through 78 or resid 80 through 311)) selection = (chain 'H' and (resid 67 through 78 or resid 80 through 311)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.340 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 42.180 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.006 0.079 44032 Z= 0.324 Angle : 0.842 17.473 59537 Z= 0.526 Chirality : 0.052 0.446 6754 Planarity : 0.004 0.069 7543 Dihedral : 13.010 100.931 16563 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.44 % Favored : 91.34 % Rotamer: Outliers : 1.04 % Allowed : 0.69 % Favored : 98.27 % Cbeta Deviations : 0.04 % 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: -1.56 (0.12), residues: 5360 helix: 0.46 (0.12), residues: 2142 sheet: -1.70 (0.18), residues: 842 loop : -2.19 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 477 TYR 0.017 0.002 TYR C 935 PHE 0.023 0.001 PHE C 531 TRP 0.037 0.002 TRP A 286 HIS 0.013 0.001 HIS C 439 Details of bonding type rmsd covalent geometry : bond 0.00592 (44032) covalent geometry : angle 0.84238 (59537) hydrogen bonds : bond 0.19355 ( 1697) hydrogen bonds : angle 6.80447 ( 4676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 342 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 ARG cc_start: 0.8022 (tpt90) cc_final: 0.7743 (tpt90) REVERT: A 1052 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8366 (mtpt) REVERT: B 422 ASP cc_start: 0.8456 (t70) cc_final: 0.8146 (t0) REVERT: B 622 LYS cc_start: 0.9588 (mmpt) cc_final: 0.9385 (mmmt) REVERT: B 984 LYS cc_start: 0.8852 (mmpt) cc_final: 0.8363 (mmmt) REVERT: B 1030 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8875 (p) REVERT: B 1124 MET cc_start: 0.8531 (ttp) cc_final: 0.8325 (ttp) REVERT: C 282 MET cc_start: 0.8239 (mtt) cc_final: 0.7742 (mtt) REVERT: C 984 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8661 (mmmt) REVERT: C 1029 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8092 (mmtm) REVERT: C 1052 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8724 (mtpt) REVERT: E 139 SER cc_start: 0.8154 (m) cc_final: 0.7922 (t) REVERT: H 301 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8856 (tm-30) REVERT: F 301 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8882 (tm-30) REVERT: G 255 MET cc_start: 0.9005 (tpp) cc_final: 0.8536 (tpt) REVERT: D 192 PHE cc_start: 0.9105 (t80) cc_final: 0.8872 (t80) REVERT: D 343 MET cc_start: 0.9276 (ttm) cc_final: 0.9000 (tpp) REVERT: D 1005 ASN cc_start: 0.8164 (m-40) cc_final: 0.7793 (p0) outliers start: 44 outliers final: 12 residues processed: 374 average time/residue: 0.2599 time to fit residues: 163.8930 Evaluate side-chains 269 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 255 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1029 LYS Chi-restraints excluded: chain C residue 1035 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 990 PRO Chi-restraints excluded: chain D residue 992 TRP Chi-restraints excluded: chain D residue 994 LYS Chi-restraints excluded: chain D residue 1030 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 265 optimal weight: 0.0270 chunk 523 optimal weight: 0.0980 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 332 GLN A 580 HIS A 618 ASN A1006 ASN A1140 GLN B 92 HIS B 337 ASN B 345 ASN B 613 ASN B 628 HIS B1008 ASN B1140 GLN C 92 HIS C1140 GLN H 277 GLN G 298 GLN D 92 HIS ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.068645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052636 restraints weight = 187978.012| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.55 r_work: 0.2964 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 44032 Z= 0.133 Angle : 0.638 9.912 59537 Z= 0.327 Chirality : 0.043 0.160 6754 Planarity : 0.004 0.054 7543 Dihedral : 6.998 102.649 5950 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.47 % Favored : 92.31 % Rotamer: Outliers : 0.77 % Allowed : 5.92 % Favored : 93.31 % 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: -1.09 (0.12), residues: 5360 helix: 0.92 (0.12), residues: 2136 sheet: -1.43 (0.19), residues: 840 loop : -2.02 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 274 TYR 0.020 0.001 TYR B1119 PHE 0.018 0.001 PHE B 192 TRP 0.017 0.002 TRP A 475 HIS 0.011 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00288 (44032) covalent geometry : angle 0.63765 (59537) hydrogen bonds : bond 0.04514 ( 1697) hydrogen bonds : angle 5.26440 ( 4676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 309 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 ARG cc_start: 0.8126 (tpt90) cc_final: 0.7911 (tpt90) REVERT: A 818 TRP cc_start: 0.8660 (t60) cc_final: 0.8370 (t60) REVERT: A 976 ILE cc_start: 0.9004 (mp) cc_final: 0.8771 (tp) REVERT: A 1052 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8453 (mtpt) REVERT: B 422 ASP cc_start: 0.8876 (t70) cc_final: 0.8562 (t0) REVERT: B 984 LYS cc_start: 0.9094 (mmpt) cc_final: 0.8476 (mmmt) REVERT: B 1124 MET cc_start: 0.9335 (ttp) cc_final: 0.9007 (ttp) REVERT: C 984 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8714 (mmtm) REVERT: C 1009 ASN cc_start: 0.8222 (t0) cc_final: 0.7615 (t0) REVERT: C 1052 LYS cc_start: 0.9111 (mtmt) cc_final: 0.8723 (mtpt) REVERT: C 1062 MET cc_start: 0.9191 (mtm) cc_final: 0.8988 (mtm) REVERT: H 301 GLU cc_start: 0.9335 (tm-30) cc_final: 0.9120 (tm-30) REVERT: F 240 LYS cc_start: 0.9203 (mmtm) cc_final: 0.8847 (mmmt) REVERT: F 301 GLU cc_start: 0.9332 (tm-30) cc_final: 0.9106 (tm-30) REVERT: D 601 ARG cc_start: 0.8692 (mmp80) cc_final: 0.8431 (mmp80) REVERT: D 862 MET cc_start: 0.9389 (mtt) cc_final: 0.9138 (mtm) REVERT: D 996 MET cc_start: 0.6477 (mmm) cc_final: 0.6184 (mmm) REVERT: D 1005 ASN cc_start: 0.8512 (m-40) cc_final: 0.7966 (p0) REVERT: D 1167 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7171 (mp0) outliers start: 31 outliers final: 17 residues processed: 331 average time/residue: 0.2480 time to fit residues: 140.8544 Evaluate side-chains 279 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 1035 ASP Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 992 TRP Chi-restraints excluded: chain D residue 995 ARG Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 484 optimal weight: 0.0970 chunk 112 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 351 optimal weight: 7.9990 chunk 480 optimal weight: 0.7980 chunk 418 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 472 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 HIS ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 346 HIS ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 ASN H 298 GLN G 298 GLN D 613 ASN D 647 GLN ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.051849 restraints weight = 203073.984| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 4.74 r_work: 0.2940 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44032 Z= 0.146 Angle : 0.591 7.899 59537 Z= 0.305 Chirality : 0.042 0.160 6754 Planarity : 0.003 0.047 7543 Dihedral : 6.524 101.445 5934 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.36 % Favored : 92.42 % Rotamer: Outliers : 1.00 % Allowed : 8.33 % Favored : 90.67 % 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: -0.91 (0.12), residues: 5360 helix: 1.13 (0.12), residues: 2148 sheet: -1.39 (0.19), residues: 836 loop : -1.99 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 141 TYR 0.010 0.001 TYR A 651 PHE 0.017 0.001 PHE B 192 TRP 0.019 0.001 TRP C 992 HIS 0.010 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00334 (44032) covalent geometry : angle 0.59103 (59537) hydrogen bonds : bond 0.03975 ( 1697) hydrogen bonds : angle 4.94274 ( 4676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 281 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8542 (mt0) REVERT: A 579 LYS cc_start: 0.9285 (mttm) cc_final: 0.9017 (mmtm) REVERT: A 818 TRP cc_start: 0.8656 (t60) cc_final: 0.8358 (t60) REVERT: A 976 ILE cc_start: 0.9118 (mp) cc_final: 0.8861 (tp) REVERT: A 996 MET cc_start: 0.8535 (ptp) cc_final: 0.8094 (pmm) REVERT: A 1052 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8456 (mtpt) REVERT: B 422 ASP cc_start: 0.8899 (t70) cc_final: 0.8581 (t0) REVERT: B 984 LYS cc_start: 0.9130 (mmpt) cc_final: 0.8755 (mmmt) REVERT: B 1124 MET cc_start: 0.9381 (ttp) cc_final: 0.9000 (ttp) REVERT: C 984 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8717 (mmtm) REVERT: C 985 ASP cc_start: 0.8863 (t0) cc_final: 0.7690 (t0) REVERT: C 987 GLN cc_start: 0.8474 (mp-120) cc_final: 0.8000 (mp10) REVERT: C 1052 LYS cc_start: 0.9120 (mtmt) cc_final: 0.8794 (mtpt) REVERT: H 240 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8787 (mmmt) REVERT: H 301 GLU cc_start: 0.9339 (tm-30) cc_final: 0.9136 (tm-30) REVERT: F 240 LYS cc_start: 0.9184 (mmtm) cc_final: 0.8825 (mmmt) REVERT: F 298 GLN cc_start: 0.8122 (pm20) cc_final: 0.7898 (pm20) REVERT: F 301 GLU cc_start: 0.9345 (tm-30) cc_final: 0.9143 (tm-30) REVERT: D 862 MET cc_start: 0.9375 (mtt) cc_final: 0.9094 (mtm) REVERT: D 1005 ASN cc_start: 0.8545 (m-40) cc_final: 0.8001 (p0) REVERT: D 1062 MET cc_start: 0.9308 (mtm) cc_final: 0.8960 (mtm) outliers start: 42 outliers final: 21 residues processed: 315 average time/residue: 0.2511 time to fit residues: 139.8613 Evaluate side-chains 289 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 267 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1035 ASP Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 238 MET Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 992 TRP Chi-restraints excluded: chain D residue 995 ARG Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1142 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 185 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 350 optimal weight: 0.6980 chunk 251 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 353 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 268 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 GLN B 336 GLN ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 ASN H 277 GLN D 875 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.069028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.052964 restraints weight = 188781.386| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 4.58 r_work: 0.2973 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44032 Z= 0.112 Angle : 0.563 11.367 59537 Z= 0.287 Chirality : 0.041 0.181 6754 Planarity : 0.003 0.057 7543 Dihedral : 6.266 103.558 5934 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.91 % Favored : 92.87 % Rotamer: Outliers : 1.23 % Allowed : 9.10 % Favored : 89.67 % 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: -0.76 (0.12), residues: 5360 helix: 1.26 (0.12), residues: 2148 sheet: -1.31 (0.19), residues: 830 loop : -1.90 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 601 TYR 0.010 0.001 TYR A 611 PHE 0.016 0.001 PHE B 192 TRP 0.020 0.001 TRP C 992 HIS 0.011 0.001 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00250 (44032) covalent geometry : angle 0.56263 (59537) hydrogen bonds : bond 0.03439 ( 1697) hydrogen bonds : angle 4.76126 ( 4676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 795 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8468 (mp10) REVERT: A 818 TRP cc_start: 0.8634 (t60) cc_final: 0.8311 (t60) REVERT: A 976 ILE cc_start: 0.9081 (mp) cc_final: 0.8841 (tp) REVERT: A 985 ASP cc_start: 0.8916 (t0) cc_final: 0.8703 (p0) REVERT: A 1052 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8706 (mtmt) REVERT: B 422 ASP cc_start: 0.8866 (t70) cc_final: 0.8537 (t0) REVERT: B 691 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7858 (pt) REVERT: B 1124 MET cc_start: 0.9346 (ttp) cc_final: 0.9018 (ttp) REVERT: B 1167 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7089 (mt-10) REVERT: C 253 SER cc_start: 0.8898 (t) cc_final: 0.8636 (p) REVERT: C 343 MET cc_start: 0.9372 (tpp) cc_final: 0.9168 (tpp) REVERT: C 601 ARG cc_start: 0.8112 (tpt90) cc_final: 0.7577 (tpt90) REVERT: C 984 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8768 (mmtm) REVERT: C 987 GLN cc_start: 0.8553 (mp-120) cc_final: 0.8269 (mm-40) REVERT: C 1052 LYS cc_start: 0.9125 (mtmt) cc_final: 0.8765 (mtpt) REVERT: C 1062 MET cc_start: 0.9187 (mtm) cc_final: 0.8935 (mtm) REVERT: H 240 LYS cc_start: 0.9217 (mmtm) cc_final: 0.8832 (mmmt) REVERT: F 240 LYS cc_start: 0.9144 (mmtm) cc_final: 0.8768 (mmmt) REVERT: F 301 GLU cc_start: 0.9319 (tm-30) cc_final: 0.9090 (tm-30) REVERT: G 240 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8533 (mmmt) REVERT: D 266 MET cc_start: 0.9365 (tpp) cc_final: 0.8934 (mpp) REVERT: D 680 GLU cc_start: 0.8600 (tt0) cc_final: 0.8284 (tt0) REVERT: D 1005 ASN cc_start: 0.8535 (m-40) cc_final: 0.8004 (p0) REVERT: D 1062 MET cc_start: 0.9298 (mtm) cc_final: 0.9042 (mtm) outliers start: 53 outliers final: 23 residues processed: 343 average time/residue: 0.2414 time to fit residues: 143.8289 Evaluate side-chains 299 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 795 GLN Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain H residue 238 MET Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1173 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 333 optimal weight: 0.3980 chunk 35 optimal weight: 9.9990 chunk 330 optimal weight: 5.9990 chunk 395 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 448 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 489 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 813 ASN ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.069175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.052956 restraints weight = 203215.798| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 4.79 r_work: 0.2969 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 44032 Z= 0.109 Angle : 0.552 10.189 59537 Z= 0.281 Chirality : 0.041 0.194 6754 Planarity : 0.003 0.044 7543 Dihedral : 6.023 104.933 5928 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.53 % Favored : 93.24 % Rotamer: Outliers : 1.19 % Allowed : 10.19 % Favored : 88.63 % 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: -0.64 (0.12), residues: 5360 helix: 1.38 (0.12), residues: 2146 sheet: -1.27 (0.19), residues: 830 loop : -1.84 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 141 TYR 0.010 0.001 TYR A 498 PHE 0.021 0.001 PHE D 192 TRP 0.012 0.001 TRP C 992 HIS 0.004 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00243 (44032) covalent geometry : angle 0.55184 (59537) hydrogen bonds : bond 0.03238 ( 1697) hydrogen bonds : angle 4.62206 ( 4676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8562 (mt0) REVERT: A 795 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8538 (mp10) REVERT: A 818 TRP cc_start: 0.8682 (t60) cc_final: 0.8314 (t60) REVERT: A 976 ILE cc_start: 0.9103 (mp) cc_final: 0.8830 (tp) REVERT: A 985 ASP cc_start: 0.8882 (t0) cc_final: 0.8680 (p0) REVERT: A 1052 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8728 (mtmt) REVERT: B 280 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8671 (t) REVERT: B 422 ASP cc_start: 0.8895 (t70) cc_final: 0.8562 (t0) REVERT: B 691 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7873 (pt) REVERT: B 984 LYS cc_start: 0.9076 (mmpt) cc_final: 0.8654 (mmmt) REVERT: B 1124 MET cc_start: 0.9385 (ttp) cc_final: 0.9029 (ttp) REVERT: B 1167 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6714 (mt-10) REVERT: C 253 SER cc_start: 0.8894 (t) cc_final: 0.8631 (p) REVERT: C 282 MET cc_start: 0.8714 (mtt) cc_final: 0.8254 (mtt) REVERT: C 343 MET cc_start: 0.9447 (tpp) cc_final: 0.9229 (tmm) REVERT: C 601 ARG cc_start: 0.8026 (tpt90) cc_final: 0.7690 (tpt90) REVERT: C 984 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8755 (mmtm) REVERT: C 1052 LYS cc_start: 0.9098 (mtmt) cc_final: 0.8708 (mtpt) REVERT: C 1062 MET cc_start: 0.9210 (mtm) cc_final: 0.8932 (mtm) REVERT: H 240 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8775 (mmmt) REVERT: F 240 LYS cc_start: 0.9129 (mmtm) cc_final: 0.8739 (mmmt) REVERT: F 301 GLU cc_start: 0.9327 (tm-30) cc_final: 0.9094 (tm-30) REVERT: G 240 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8538 (mmmt) REVERT: D 280 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8698 (t) REVERT: D 680 GLU cc_start: 0.8617 (tt0) cc_final: 0.8290 (tt0) REVERT: D 1005 ASN cc_start: 0.8561 (m-40) cc_final: 0.8025 (p0) REVERT: D 1094 LYS cc_start: 0.9397 (mttt) cc_final: 0.9124 (mtmm) REVERT: D 1167 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7677 (mp0) outliers start: 51 outliers final: 25 residues processed: 335 average time/residue: 0.2378 time to fit residues: 138.5059 Evaluate side-chains 306 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 795 GLN Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain H residue 238 MET Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 504 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 351 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.068798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.052712 restraints weight = 192360.386| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.63 r_work: 0.2970 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44032 Z= 0.122 Angle : 0.552 10.252 59537 Z= 0.281 Chirality : 0.041 0.217 6754 Planarity : 0.003 0.043 7543 Dihedral : 5.942 104.683 5928 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.87 % Favored : 92.91 % Rotamer: Outliers : 1.31 % Allowed : 10.75 % Favored : 87.94 % 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: -0.58 (0.12), residues: 5360 helix: 1.48 (0.12), residues: 2136 sheet: -1.27 (0.19), residues: 832 loop : -1.83 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 601 TYR 0.019 0.001 TYR B1119 PHE 0.023 0.001 PHE D 192 TRP 0.024 0.001 TRP C 992 HIS 0.004 0.001 HIS B1157 Details of bonding type rmsd covalent geometry : bond 0.00277 (44032) covalent geometry : angle 0.55208 (59537) hydrogen bonds : bond 0.03227 ( 1697) hydrogen bonds : angle 4.55574 ( 4676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8575 (mt0) REVERT: A 795 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8485 (mp10) REVERT: A 818 TRP cc_start: 0.8667 (t60) cc_final: 0.8284 (t60) REVERT: A 976 ILE cc_start: 0.9087 (mp) cc_final: 0.8828 (tp) REVERT: A 1052 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8478 (mtpt) REVERT: B 280 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8700 (t) REVERT: B 422 ASP cc_start: 0.8903 (t70) cc_final: 0.8564 (t0) REVERT: B 720 THR cc_start: 0.8914 (p) cc_final: 0.8538 (t) REVERT: B 984 LYS cc_start: 0.9070 (mmpt) cc_final: 0.8640 (mmmt) REVERT: B 1124 MET cc_start: 0.9372 (ttp) cc_final: 0.8991 (ttp) REVERT: C 253 SER cc_start: 0.8884 (t) cc_final: 0.8611 (p) REVERT: C 601 ARG cc_start: 0.7984 (tpt90) cc_final: 0.7613 (tpt90) REVERT: C 984 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8756 (mmtm) REVERT: C 1119 TYR cc_start: 0.8728 (p90) cc_final: 0.8426 (p90) REVERT: H 240 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8748 (mmmt) REVERT: F 240 LYS cc_start: 0.9123 (mmtm) cc_final: 0.8725 (mmmt) REVERT: F 301 GLU cc_start: 0.9316 (tm-30) cc_final: 0.9079 (tm-30) REVERT: G 240 LYS cc_start: 0.9013 (mmtm) cc_final: 0.8554 (mmmt) REVERT: D 280 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8732 (t) REVERT: D 680 GLU cc_start: 0.8628 (tt0) cc_final: 0.8275 (tt0) REVERT: D 967 LEU cc_start: 0.8278 (tp) cc_final: 0.8046 (tp) REVERT: D 1005 ASN cc_start: 0.8552 (m-40) cc_final: 0.8020 (p0) REVERT: D 1094 LYS cc_start: 0.9366 (mttt) cc_final: 0.9104 (mtmm) REVERT: D 1167 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7678 (mp0) outliers start: 57 outliers final: 33 residues processed: 336 average time/residue: 0.2330 time to fit residues: 136.6727 Evaluate side-chains 310 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 273 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 795 GLN Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1192 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1142 THR Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 238 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 894 MET Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1140 GLN Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1173 LEU Chi-restraints excluded: chain D residue 1192 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 152 optimal weight: 3.9990 chunk 306 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 481 optimal weight: 0.0670 chunk 4 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 505 optimal weight: 3.9990 chunk 334 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 501 optimal weight: 4.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN D 336 GLN ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.066594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.050522 restraints weight = 190290.329| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.64 r_work: 0.2901 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 44032 Z= 0.194 Angle : 0.595 9.167 59537 Z= 0.303 Chirality : 0.042 0.270 6754 Planarity : 0.003 0.044 7543 Dihedral : 6.045 102.155 5928 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.52 % Favored : 92.25 % Rotamer: Outliers : 1.40 % Allowed : 11.10 % Favored : 87.50 % 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: -0.61 (0.12), residues: 5360 helix: 1.44 (0.12), residues: 2152 sheet: -1.26 (0.19), residues: 832 loop : -1.87 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1058 TYR 0.013 0.001 TYR A 577 PHE 0.029 0.001 PHE D 192 TRP 0.012 0.001 TRP C 992 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00445 (44032) covalent geometry : angle 0.59501 (59537) hydrogen bonds : bond 0.03474 ( 1697) hydrogen bonds : angle 4.61314 ( 4676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 274 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: A 339 MET cc_start: 0.9082 (tmm) cc_final: 0.8736 (tmm) REVERT: A 795 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: A 818 TRP cc_start: 0.8718 (t60) cc_final: 0.8268 (t60) REVERT: A 976 ILE cc_start: 0.9182 (mp) cc_final: 0.8956 (tp) REVERT: A 1052 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8524 (mtpt) REVERT: B 280 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8776 (t) REVERT: B 422 ASP cc_start: 0.8942 (t70) cc_final: 0.8609 (t0) REVERT: B 720 THR cc_start: 0.8946 (p) cc_final: 0.8555 (t) REVERT: B 984 LYS cc_start: 0.9032 (mmpt) cc_final: 0.8590 (mmmt) REVERT: B 1124 MET cc_start: 0.9387 (ttp) cc_final: 0.8925 (ttp) REVERT: C 253 SER cc_start: 0.8919 (t) cc_final: 0.8673 (p) REVERT: C 601 ARG cc_start: 0.8065 (tpt90) cc_final: 0.7814 (tpt90) REVERT: C 984 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8641 (mmtm) REVERT: C 1052 LYS cc_start: 0.9107 (mtmt) cc_final: 0.8712 (mtpt) REVERT: C 1062 MET cc_start: 0.9240 (mtm) cc_final: 0.8978 (mtm) REVERT: C 1119 TYR cc_start: 0.8809 (p90) cc_final: 0.8561 (p90) REVERT: H 240 LYS cc_start: 0.9162 (mmtm) cc_final: 0.8743 (mmmt) REVERT: F 240 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8716 (mmmt) REVERT: F 301 GLU cc_start: 0.9357 (tm-30) cc_final: 0.9094 (tm-30) REVERT: G 240 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8581 (mmmt) REVERT: D 280 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8823 (t) REVERT: D 967 LEU cc_start: 0.8168 (tp) cc_final: 0.7917 (tp) REVERT: D 1005 ASN cc_start: 0.8599 (m-40) cc_final: 0.8000 (p0) REVERT: D 1062 MET cc_start: 0.9414 (mtm) cc_final: 0.9048 (mtm) REVERT: D 1094 LYS cc_start: 0.9340 (mttt) cc_final: 0.9094 (mtmm) outliers start: 61 outliers final: 38 residues processed: 325 average time/residue: 0.2360 time to fit residues: 133.3393 Evaluate side-chains 308 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 795 GLN Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1192 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1109 CYS Chi-restraints excluded: chain C residue 1142 THR Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 238 MET Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 894 MET Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1173 LEU Chi-restraints excluded: chain D residue 1192 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 220 optimal weight: 7.9990 chunk 375 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 388 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 292 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS H 277 GLN ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.068071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051805 restraints weight = 207194.836| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.81 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 44032 Z= 0.135 Angle : 0.563 8.779 59537 Z= 0.287 Chirality : 0.041 0.165 6754 Planarity : 0.003 0.043 7543 Dihedral : 5.958 100.251 5928 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.87 % Favored : 92.91 % Rotamer: Outliers : 1.29 % Allowed : 11.46 % Favored : 87.25 % 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: -0.58 (0.12), residues: 5360 helix: 1.45 (0.12), residues: 2150 sheet: -1.27 (0.19), residues: 836 loop : -1.83 (0.13), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 141 TYR 0.010 0.001 TYR A 498 PHE 0.019 0.001 PHE D 192 TRP 0.011 0.001 TRP C 992 HIS 0.005 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00309 (44032) covalent geometry : angle 0.56262 (59537) hydrogen bonds : bond 0.03273 ( 1697) hydrogen bonds : angle 4.54620 ( 4676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8430 (mt0) REVERT: A 339 MET cc_start: 0.9028 (tmm) cc_final: 0.8677 (tmm) REVERT: A 795 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: A 818 TRP cc_start: 0.8386 (t60) cc_final: 0.7918 (t60) REVERT: A 976 ILE cc_start: 0.9077 (mp) cc_final: 0.8870 (tp) REVERT: A 1052 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8374 (mtpt) REVERT: B 280 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8644 (t) REVERT: B 422 ASP cc_start: 0.8707 (t70) cc_final: 0.8351 (t0) REVERT: B 720 THR cc_start: 0.8896 (p) cc_final: 0.8532 (t) REVERT: B 1124 MET cc_start: 0.8855 (ttp) cc_final: 0.8414 (ttp) REVERT: C 253 SER cc_start: 0.8943 (t) cc_final: 0.8713 (p) REVERT: C 984 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8528 (mmtm) REVERT: C 1052 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8546 (mtpt) REVERT: C 1062 MET cc_start: 0.8911 (mtm) cc_final: 0.8657 (mtm) REVERT: C 1119 TYR cc_start: 0.8473 (p90) cc_final: 0.8200 (p90) REVERT: H 240 LYS cc_start: 0.9111 (mmtm) cc_final: 0.8634 (mmmt) REVERT: F 240 LYS cc_start: 0.9104 (mmtm) cc_final: 0.8701 (mmmt) REVERT: F 301 GLU cc_start: 0.9315 (tm-30) cc_final: 0.9062 (tm-30) REVERT: G 240 LYS cc_start: 0.9035 (mmtm) cc_final: 0.8563 (mmmt) REVERT: D 280 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8674 (t) REVERT: D 967 LEU cc_start: 0.8096 (tp) cc_final: 0.7878 (tp) REVERT: D 1005 ASN cc_start: 0.8481 (m-40) cc_final: 0.7959 (p0) REVERT: D 1062 MET cc_start: 0.9252 (mtm) cc_final: 0.8849 (mtm) REVERT: D 1094 LYS cc_start: 0.9276 (mttt) cc_final: 0.9042 (mtmm) REVERT: D 1167 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7584 (mp0) outliers start: 56 outliers final: 39 residues processed: 328 average time/residue: 0.2360 time to fit residues: 135.4256 Evaluate side-chains 317 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 795 GLN Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1109 CYS Chi-restraints excluded: chain C residue 1142 THR Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 894 MET Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1173 LEU Chi-restraints excluded: chain D residue 1192 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 209 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 345 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 348 optimal weight: 0.3980 chunk 490 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1140 GLN ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.068546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.052617 restraints weight = 180642.779| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.47 r_work: 0.2965 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44032 Z= 0.118 Angle : 0.556 9.446 59537 Z= 0.282 Chirality : 0.041 0.257 6754 Planarity : 0.003 0.045 7543 Dihedral : 5.872 100.673 5928 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.93 % Favored : 92.85 % Rotamer: Outliers : 1.21 % Allowed : 11.69 % Favored : 87.11 % 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: -0.53 (0.12), residues: 5360 helix: 1.48 (0.12), residues: 2150 sheet: -1.23 (0.19), residues: 844 loop : -1.79 (0.13), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 141 TYR 0.010 0.001 TYR A 498 PHE 0.016 0.001 PHE B 192 TRP 0.011 0.001 TRP A 475 HIS 0.005 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00268 (44032) covalent geometry : angle 0.55610 (59537) hydrogen bonds : bond 0.03182 ( 1697) hydrogen bonds : angle 4.49421 ( 4676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 278 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8581 (mt0) REVERT: A 339 MET cc_start: 0.9094 (tmm) cc_final: 0.8761 (tmm) REVERT: A 645 ARG cc_start: 0.9048 (mmt90) cc_final: 0.8660 (tpp80) REVERT: A 795 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8485 (mp10) REVERT: A 818 TRP cc_start: 0.8686 (t60) cc_final: 0.8362 (t60) REVERT: A 976 ILE cc_start: 0.9129 (mp) cc_final: 0.8885 (tp) REVERT: A 1052 LYS cc_start: 0.8968 (mtmt) cc_final: 0.8554 (mtpt) REVERT: B 280 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8717 (t) REVERT: B 422 ASP cc_start: 0.8909 (t70) cc_final: 0.8641 (t0) REVERT: B 720 THR cc_start: 0.8924 (p) cc_final: 0.8539 (t) REVERT: B 984 LYS cc_start: 0.9026 (mmpt) cc_final: 0.8633 (mmmt) REVERT: B 1124 MET cc_start: 0.9348 (ttp) cc_final: 0.8925 (ttp) REVERT: C 253 SER cc_start: 0.8892 (t) cc_final: 0.8640 (p) REVERT: C 984 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8693 (mmtm) REVERT: C 987 GLN cc_start: 0.8277 (tp40) cc_final: 0.8035 (mm-40) REVERT: C 1009 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7481 (p0) REVERT: C 1052 LYS cc_start: 0.9076 (mtmt) cc_final: 0.8655 (mtpt) REVERT: C 1062 MET cc_start: 0.9230 (mtm) cc_final: 0.8981 (mtm) REVERT: C 1119 TYR cc_start: 0.8808 (p90) cc_final: 0.8568 (p90) REVERT: H 240 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8674 (mmmt) REVERT: H 255 MET cc_start: 0.9003 (tpp) cc_final: 0.8007 (tpp) REVERT: F 240 LYS cc_start: 0.9089 (mmtm) cc_final: 0.8694 (mmmt) REVERT: F 301 GLU cc_start: 0.9330 (tm-30) cc_final: 0.9080 (tm-30) REVERT: G 240 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8553 (mmmt) REVERT: D 280 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8728 (t) REVERT: D 343 MET cc_start: 0.9295 (ttm) cc_final: 0.9002 (tpp) REVERT: D 1005 ASN cc_start: 0.8575 (m-40) cc_final: 0.8125 (p0) REVERT: D 1062 MET cc_start: 0.9438 (mtm) cc_final: 0.9125 (mtm) REVERT: D 1094 LYS cc_start: 0.9331 (mttt) cc_final: 0.9098 (mtmm) REVERT: D 1167 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7644 (mp0) outliers start: 52 outliers final: 38 residues processed: 323 average time/residue: 0.2433 time to fit residues: 136.6563 Evaluate side-chains 307 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 264 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 795 GLN Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1192 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1009 ASN Chi-restraints excluded: chain C residue 1109 CYS Chi-restraints excluded: chain C residue 1142 THR Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 894 MET Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1173 LEU Chi-restraints excluded: chain D residue 1192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 476 optimal weight: 8.9990 chunk 317 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 336 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 chunk 162 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 203 optimal weight: 0.0030 chunk 54 optimal weight: 3.9990 chunk 410 optimal weight: 0.7980 chunk 121 optimal weight: 0.1980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.069871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.053804 restraints weight = 191169.088| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 4.66 r_work: 0.2995 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 44032 Z= 0.097 Angle : 0.549 9.196 59537 Z= 0.277 Chirality : 0.041 0.232 6754 Planarity : 0.003 0.048 7543 Dihedral : 5.714 102.341 5928 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.14 % Favored : 93.63 % Rotamer: Outliers : 1.04 % Allowed : 11.94 % Favored : 87.02 % 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: -0.45 (0.12), residues: 5360 helix: 1.56 (0.12), residues: 2134 sheet: -1.22 (0.19), residues: 846 loop : -1.71 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 141 TYR 0.018 0.001 TYR B1119 PHE 0.015 0.001 PHE B 192 TRP 0.013 0.001 TRP D 992 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00214 (44032) covalent geometry : angle 0.54901 (59537) hydrogen bonds : bond 0.02978 ( 1697) hydrogen bonds : angle 4.41069 ( 4676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 299 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.9241 (tp) cc_final: 0.8995 (tp) REVERT: A 332 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8540 (mt0) REVERT: A 645 ARG cc_start: 0.9049 (mmt90) cc_final: 0.8552 (tpp80) REVERT: A 818 TRP cc_start: 0.8647 (t60) cc_final: 0.8444 (t60) REVERT: A 996 MET cc_start: 0.8124 (ptp) cc_final: 0.7513 (pmm) REVERT: A 1134 GLN cc_start: 0.8840 (mp10) cc_final: 0.8447 (mp10) REVERT: B 280 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8631 (t) REVERT: B 422 ASP cc_start: 0.8872 (t70) cc_final: 0.8592 (t0) REVERT: B 720 THR cc_start: 0.8870 (p) cc_final: 0.8476 (t) REVERT: B 984 LYS cc_start: 0.9034 (mmpt) cc_final: 0.8681 (mmmt) REVERT: B 1124 MET cc_start: 0.9381 (ttp) cc_final: 0.8968 (ttp) REVERT: C 253 SER cc_start: 0.8883 (t) cc_final: 0.8624 (p) REVERT: C 517 ASN cc_start: 0.8603 (t0) cc_final: 0.8390 (t0) REVERT: C 818 TRP cc_start: 0.8610 (t60) cc_final: 0.8356 (t60) REVERT: C 984 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8613 (mmtm) REVERT: C 987 GLN cc_start: 0.8222 (tp40) cc_final: 0.7532 (mm-40) REVERT: C 1009 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.6328 (p0) REVERT: C 1052 LYS cc_start: 0.9101 (mtmt) cc_final: 0.8667 (mtpt) REVERT: C 1062 MET cc_start: 0.9213 (mtm) cc_final: 0.8995 (mtm) REVERT: C 1119 TYR cc_start: 0.8810 (p90) cc_final: 0.8574 (p90) REVERT: H 240 LYS cc_start: 0.9108 (mmtm) cc_final: 0.8611 (mmmt) REVERT: H 242 ASP cc_start: 0.9147 (p0) cc_final: 0.8876 (m-30) REVERT: F 240 LYS cc_start: 0.9082 (mmtm) cc_final: 0.8683 (mmmt) REVERT: F 301 GLU cc_start: 0.9330 (tm-30) cc_final: 0.9074 (tm-30) REVERT: G 240 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8562 (mmmt) REVERT: D 280 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8668 (t) REVERT: D 680 GLU cc_start: 0.8625 (tt0) cc_final: 0.8267 (tt0) REVERT: D 893 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8918 (tp) REVERT: D 1005 ASN cc_start: 0.8574 (m-40) cc_final: 0.8045 (p0) REVERT: D 1094 LYS cc_start: 0.9313 (mttt) cc_final: 0.9074 (mtmm) REVERT: D 1167 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7673 (mp0) outliers start: 44 outliers final: 32 residues processed: 337 average time/residue: 0.2430 time to fit residues: 142.9634 Evaluate side-chains 315 residues out of total 4856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 1009 ASN Chi-restraints excluded: chain C residue 1109 CYS Chi-restraints excluded: chain C residue 1142 THR Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1062 MET Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1173 LEU Chi-restraints excluded: chain D residue 1192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 428 optimal weight: 7.9990 chunk 358 optimal weight: 2.9990 chunk 323 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 118 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 284 optimal weight: 0.9990 chunk 457 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 501 optimal weight: 0.3980 chunk 131 optimal weight: 0.8980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN G 277 GLN ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.069913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.053887 restraints weight = 187978.414| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 4.62 r_work: 0.2999 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 44032 Z= 0.100 Angle : 0.550 8.797 59537 Z= 0.275 Chirality : 0.041 0.214 6754 Planarity : 0.003 0.047 7543 Dihedral : 5.646 103.832 5928 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.24 % Favored : 93.54 % Rotamer: Outliers : 1.00 % Allowed : 12.43 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.12), residues: 5360 helix: 1.59 (0.12), residues: 2134 sheet: -1.19 (0.19), residues: 846 loop : -1.67 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 141 TYR 0.027 0.001 TYR G 310 PHE 0.015 0.001 PHE B 192 TRP 0.010 0.001 TRP D 992 HIS 0.004 0.001 HIS C1157 Details of bonding type rmsd covalent geometry : bond 0.00225 (44032) covalent geometry : angle 0.55033 (59537) hydrogen bonds : bond 0.02938 ( 1697) hydrogen bonds : angle 4.37028 ( 4676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13003.96 seconds wall clock time: 223 minutes 46.12 seconds (13426.12 seconds total)