Starting phenix.real_space_refine on Thu Jul 31 03:25:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f1d_28795/07_2025/8f1d_28795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f1d_28795/07_2025/8f1d_28795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f1d_28795/07_2025/8f1d_28795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f1d_28795/07_2025/8f1d_28795.map" model { file = "/net/cci-nas-00/data/ceres_data/8f1d_28795/07_2025/8f1d_28795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f1d_28795/07_2025/8f1d_28795.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 Zn 4 6.06 5 S 68 5.16 5 C 8484 2.51 5 N 2152 2.21 5 O 2176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12888 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3192 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3192 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3192 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3192 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 33 Unusual residues: {' K': 4, ' ZN': 1, 'CLR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' ZN': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' ZN': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' ZN': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 800 SG CYS A 104 66.035 80.119 76.719 1.00193.00 S ATOM 806 SG CYS A 105 62.642 78.693 77.855 1.00202.39 S ATOM 3823 SG CYS B 83 65.774 76.456 77.997 1.00207.60 S ATOM 3992 SG CYS B 104 80.119 65.001 76.713 1.00193.69 S ATOM 3998 SG CYS B 105 78.699 68.394 77.855 1.00202.98 S ATOM 7015 SG CYS C 83 76.457 65.265 77.996 1.00206.73 S ATOM 7184 SG CYS C 104 65.002 50.920 76.716 1.00193.64 S ATOM 7190 SG CYS C 105 68.394 52.343 77.858 1.00202.41 S ATOM 10207 SG CYS D 83 65.264 54.584 77.994 1.00206.45 S ATOM 631 SG CYS A 83 54.583 65.775 77.995 1.00206.51 S ATOM 10376 SG CYS D 104 50.921 66.039 76.712 1.00194.05 S ATOM 10382 SG CYS D 105 52.340 62.646 77.854 1.00201.59 S Time building chain proxies: 8.62, per 1000 atoms: 0.67 Number of scatterers: 12888 At special positions: 0 Unit cell: (131.88, 131.88, 124.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 K 4 19.00 S 68 16.00 O 2176 8.00 N 2152 7.00 C 8484 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: 3.73 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 105 " pdb="ZN ZN A 601 " - pdb=" SG CYS B 83 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 104 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 105 " pdb="ZN ZN B 601 " - pdb=" SG CYS C 83 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 601 " - pdb=" SG CYS D 83 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 104 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 105 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" SG CYS A 83 " Number of angles added : 12 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 4 sheets defined 68.5% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.811A pdb=" N ILE A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.748A pdb=" N VAL A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.587A pdb=" N TRP A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.816A pdb=" N ALA A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.505A pdb=" N PHE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 210 removed outlier: 3.764A pdb=" N TYR A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 removed outlier: 3.964A pdb=" N GLU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 276 through 295 removed outlier: 3.688A pdb=" N ILE A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Proline residue: A 288 - end of helix Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 320 through 325 removed outlier: 4.238A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 340 Processing helix chain 'A' and resid 341 through 367 removed outlier: 3.602A pdb=" N PHE A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 removed outlier: 4.005A pdb=" N TRP A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 removed outlier: 3.920A pdb=" N LEU A 415 " --> pdb=" O TRP A 411 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 452 removed outlier: 3.675A pdb=" N LYS A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 63 through 74 removed outlier: 3.811A pdb=" N ILE B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.531A pdb=" N ASP B 100 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.588A pdb=" N TRP B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.818A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 187 through 210 removed outlier: 3.753A pdb=" N TYR B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 266 removed outlier: 3.969A pdb=" N GLU B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 276 through 295 removed outlier: 3.689A pdb=" N ILE B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) Proline residue: B 288 - end of helix Processing helix chain 'B' and resid 299 through 314 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 320 through 325 removed outlier: 4.218A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 341 through 367 removed outlier: 3.603A pdb=" N PHE B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.005A pdb=" N TRP B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 removed outlier: 3.924A pdb=" N LEU B 415 " --> pdb=" O TRP B 411 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 452 removed outlier: 3.683A pdb=" N LYS B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.810A pdb=" N ILE C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.509A pdb=" N ASP C 100 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.587A pdb=" N TRP C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 119 removed outlier: 3.820A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.504A pdb=" N PHE C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 210 removed outlier: 3.771A pdb=" N TYR C 191 " --> pdb=" O ARG C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 266 removed outlier: 4.005A pdb=" N GLU C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'C' and resid 276 through 295 removed outlier: 3.689A pdb=" N ILE C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Proline residue: C 288 - end of helix Processing helix chain 'C' and resid 299 through 314 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 320 through 325 removed outlier: 4.236A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 340 Processing helix chain 'C' and resid 341 through 367 removed outlier: 3.597A pdb=" N PHE C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 399 removed outlier: 4.005A pdb=" N TRP C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 removed outlier: 3.915A pdb=" N LEU C 415 " --> pdb=" O TRP C 411 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 452 removed outlier: 3.672A pdb=" N LYS C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.812A pdb=" N ILE D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.531A pdb=" N ASP D 100 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 101 " --> pdb=" O GLU D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.588A pdb=" N TRP D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 119 removed outlier: 3.817A pdb=" N ALA D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.501A pdb=" N PHE D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 210 removed outlier: 3.761A pdb=" N TYR D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 266 removed outlier: 3.963A pdb=" N GLU D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE D 266 " --> pdb=" O MET D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 276 through 295 removed outlier: 3.689A pdb=" N ILE D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) Proline residue: D 288 - end of helix Processing helix chain 'D' and resid 299 through 314 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 320 through 325 removed outlier: 4.237A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 340 Processing helix chain 'D' and resid 341 through 367 removed outlier: 3.598A pdb=" N PHE D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 399 removed outlier: 4.006A pdb=" N TRP D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 removed outlier: 3.924A pdb=" N LEU D 415 " --> pdb=" O TRP D 411 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 416 " --> pdb=" O SER D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 452 removed outlier: 3.635A pdb=" N LYS D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 452 " --> pdb=" O ALA D 448 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.951A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP A 49 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.514A pdb=" N PHE B 55 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP B 49 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 22 removed outlier: 3.517A pdb=" N PHE C 55 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP C 49 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 22 removed outlier: 3.515A pdb=" N PHE D 55 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP D 49 " --> pdb=" O GLU D 54 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 2010 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: 3.93 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3978 1.34 - 1.46: 2748 1.46 - 1.57: 6446 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 13276 Sorted by residual: bond pdb=" C MET B 430 " pdb=" N PRO B 431 " ideal model delta sigma weight residual 1.336 1.366 -0.031 9.80e-03 1.04e+04 9.70e+00 bond pdb=" C MET C 430 " pdb=" N PRO C 431 " ideal model delta sigma weight residual 1.336 1.366 -0.031 9.80e-03 1.04e+04 9.70e+00 bond pdb=" C MET A 430 " pdb=" N PRO A 431 " ideal model delta sigma weight residual 1.336 1.366 -0.030 9.80e-03 1.04e+04 9.53e+00 bond pdb=" C MET D 430 " pdb=" N PRO D 431 " ideal model delta sigma weight residual 1.336 1.366 -0.030 9.80e-03 1.04e+04 9.45e+00 bond pdb=" N LYS A 457 " pdb=" CA LYS A 457 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.17e-01 ... (remaining 13271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 17575 1.25 - 2.50: 372 2.50 - 3.75: 95 3.75 - 5.01: 18 5.01 - 6.26: 12 Bond angle restraints: 18072 Sorted by residual: angle pdb=" CA PRO D 431 " pdb=" C PRO D 431 " pdb=" O PRO D 431 " ideal model delta sigma weight residual 118.78 121.55 -2.77 1.40e+00 5.10e-01 3.92e+00 angle pdb=" CA PRO C 431 " pdb=" C PRO C 431 " pdb=" O PRO C 431 " ideal model delta sigma weight residual 118.78 121.54 -2.76 1.40e+00 5.10e-01 3.88e+00 angle pdb=" CA PRO A 431 " pdb=" C PRO A 431 " pdb=" O PRO A 431 " ideal model delta sigma weight residual 118.78 121.54 -2.76 1.40e+00 5.10e-01 3.88e+00 angle pdb=" CA PRO B 431 " pdb=" C PRO B 431 " pdb=" O PRO B 431 " ideal model delta sigma weight residual 118.78 121.50 -2.72 1.40e+00 5.10e-01 3.77e+00 angle pdb=" N LEU B 287 " pdb=" CA LEU B 287 " pdb=" C LEU B 287 " ideal model delta sigma weight residual 112.75 115.33 -2.58 1.36e+00 5.41e-01 3.60e+00 ... (remaining 18067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 7392 16.27 - 32.53: 431 32.53 - 48.80: 73 48.80 - 65.07: 8 65.07 - 81.33: 4 Dihedral angle restraints: 7908 sinusoidal: 3300 harmonic: 4608 Sorted by residual: dihedral pdb=" N LEU C 245 " pdb=" CA LEU C 245 " pdb=" CB LEU C 245 " pdb=" CG LEU C 245 " ideal model delta sinusoidal sigma weight residual -60.00 -118.99 58.99 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU D 245 " pdb=" CA LEU D 245 " pdb=" CB LEU D 245 " pdb=" CG LEU D 245 " ideal model delta sinusoidal sigma weight residual -60.00 -118.15 58.15 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LEU A 245 " pdb=" CA LEU A 245 " pdb=" CB LEU A 245 " pdb=" CG LEU A 245 " ideal model delta sinusoidal sigma weight residual -60.00 -118.10 58.10 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 7905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1136 0.028 - 0.056: 583 0.056 - 0.085: 174 0.085 - 0.113: 76 0.113 - 0.141: 23 Chirality restraints: 1992 Sorted by residual: chirality pdb=" CA MET B 430 " pdb=" N MET B 430 " pdb=" C MET B 430 " pdb=" CB MET B 430 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA MET A 430 " pdb=" N MET A 430 " pdb=" C MET A 430 " pdb=" CB MET A 430 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA MET C 430 " pdb=" N MET C 430 " pdb=" C MET C 430 " pdb=" CB MET C 430 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1989 not shown) Planarity restraints: 2244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 84 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO D 85 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 85 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 85 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 84 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO B 85 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 84 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 85 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.024 5.00e-02 4.00e+02 ... (remaining 2241 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.89: 4861 2.89 - 3.45: 14916 3.45 - 4.01: 22112 4.01 - 4.58: 32522 4.58 - 5.14: 45463 Nonbonded interactions: 119874 Sorted by model distance: nonbonded pdb=" NH1 ARG C 33 " pdb=" O PHE C 93 " model vdw 2.321 3.120 nonbonded pdb=" NH1 ARG A 33 " pdb=" O PHE A 93 " model vdw 2.322 3.120 nonbonded pdb=" NH1 ARG D 33 " pdb=" O PHE D 93 " model vdw 2.322 3.120 nonbonded pdb=" NH1 ARG B 33 " pdb=" O PHE B 93 " model vdw 2.323 3.120 nonbonded pdb=" O THR D 399 " pdb=" OG1 THR D 400 " model vdw 2.416 3.040 ... (remaining 119869 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 7 through 463 or resid 601 through 602)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.150 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 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 : 0.004 0.044 13292 Z= 0.189 Angle : 0.510 6.258 18084 Z= 0.259 Chirality : 0.039 0.141 1992 Planarity : 0.004 0.043 2244 Dihedral : 10.401 81.332 4932 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.59 % Allowed : 5.04 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.22), residues: 1552 helix: 1.63 (0.17), residues: 948 sheet: 1.46 (0.82), residues: 40 loop : -0.84 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 392 HIS 0.002 0.001 HIS C 66 PHE 0.007 0.001 PHE D 244 TYR 0.008 0.001 TYR B 365 ARG 0.002 0.000 ARG C 320 Details of bonding type rmsd hydrogen bonds : bond 0.16980 ( 687) hydrogen bonds : angle 5.64301 ( 2010) metal coordination : bond 0.01222 ( 16) metal coordination : angle 1.15211 ( 12) covalent geometry : bond 0.00428 (13276) covalent geometry : angle 0.50907 (18072) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 1.459 Fit side-chains REVERT: A 182 ASP cc_start: 0.7001 (t0) cc_final: 0.6703 (t0) REVERT: A 213 GLU cc_start: 0.5954 (mp0) cc_final: 0.5674 (mp0) REVERT: A 275 LYS cc_start: 0.7147 (mttt) cc_final: 0.6472 (tptt) REVERT: A 295 LEU cc_start: 0.6683 (tp) cc_final: 0.6439 (tt) REVERT: A 339 ARG cc_start: 0.6814 (ttp-170) cc_final: 0.6609 (ttm110) REVERT: A 437 ASN cc_start: 0.6283 (t0) cc_final: 0.5941 (m-40) REVERT: A 451 LYS cc_start: 0.6797 (mmpt) cc_final: 0.6411 (mttt) REVERT: A 457 LYS cc_start: 0.6164 (pttt) cc_final: 0.5791 (tptm) REVERT: A 458 LYS cc_start: 0.6502 (mmmt) cc_final: 0.6220 (mtmt) REVERT: B 182 ASP cc_start: 0.7006 (t0) cc_final: 0.6709 (t0) REVERT: B 213 GLU cc_start: 0.5885 (mp0) cc_final: 0.5565 (mp0) REVERT: B 275 LYS cc_start: 0.7156 (mttt) cc_final: 0.6481 (tptt) REVERT: B 295 LEU cc_start: 0.6713 (tp) cc_final: 0.6453 (tt) REVERT: B 339 ARG cc_start: 0.6807 (ttp-170) cc_final: 0.6597 (ttm110) REVERT: B 437 ASN cc_start: 0.6269 (t0) cc_final: 0.5928 (m-40) REVERT: B 451 LYS cc_start: 0.6707 (mmpt) cc_final: 0.6316 (mttt) REVERT: B 458 LYS cc_start: 0.6551 (mmmt) cc_final: 0.6178 (ttpt) REVERT: C 182 ASP cc_start: 0.7000 (t0) cc_final: 0.6703 (t0) REVERT: C 213 GLU cc_start: 0.5875 (mp0) cc_final: 0.5562 (mp0) REVERT: C 275 LYS cc_start: 0.7116 (mttt) cc_final: 0.6396 (tptt) REVERT: C 295 LEU cc_start: 0.6699 (tp) cc_final: 0.6444 (tt) REVERT: C 339 ARG cc_start: 0.6763 (ttp-170) cc_final: 0.6559 (ttm110) REVERT: C 437 ASN cc_start: 0.6287 (t0) cc_final: 0.5947 (m-40) REVERT: C 451 LYS cc_start: 0.6786 (mmpt) cc_final: 0.6401 (mttt) REVERT: C 457 LYS cc_start: 0.6187 (pttt) cc_final: 0.5814 (tmtt) REVERT: C 458 LYS cc_start: 0.6533 (mmmt) cc_final: 0.6241 (mtmt) REVERT: D 182 ASP cc_start: 0.7004 (t0) cc_final: 0.6707 (t0) REVERT: D 213 GLU cc_start: 0.5960 (mp0) cc_final: 0.5677 (mp0) REVERT: D 275 LYS cc_start: 0.7144 (mttt) cc_final: 0.6471 (tptt) REVERT: D 295 LEU cc_start: 0.6693 (tp) cc_final: 0.6428 (tt) REVERT: D 339 ARG cc_start: 0.6771 (ttp-170) cc_final: 0.6568 (ttm110) REVERT: D 437 ASN cc_start: 0.6314 (t0) cc_final: 0.5970 (m-40) REVERT: D 451 LYS cc_start: 0.6793 (mmpt) cc_final: 0.6404 (mttt) REVERT: D 457 LYS cc_start: 0.6301 (pttt) cc_final: 0.5892 (tptm) REVERT: D 458 LYS cc_start: 0.6463 (mmmt) cc_final: 0.6252 (mtpt) outliers start: 8 outliers final: 0 residues processed: 231 average time/residue: 1.1825 time to fit residues: 298.8420 Evaluate side-chains 159 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS B 43 HIS C 43 HIS D 43 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.194923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.131312 restraints weight = 14482.774| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.93 r_work: 0.2925 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13292 Z= 0.250 Angle : 0.671 9.579 18084 Z= 0.335 Chirality : 0.047 0.146 1992 Planarity : 0.005 0.047 2244 Dihedral : 5.051 38.269 1996 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.78 % Allowed : 10.24 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1552 helix: 1.20 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -0.86 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 392 HIS 0.004 0.001 HIS A 383 PHE 0.017 0.002 PHE D 56 TYR 0.014 0.002 TYR D 365 ARG 0.006 0.001 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.08026 ( 687) hydrogen bonds : angle 4.81563 ( 2010) metal coordination : bond 0.01327 ( 16) metal coordination : angle 2.44266 ( 12) covalent geometry : bond 0.00629 (13276) covalent geometry : angle 0.66872 (18072) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.389 Fit side-chains REVERT: A 182 ASP cc_start: 0.7346 (t70) cc_final: 0.7028 (t0) REVERT: A 275 LYS cc_start: 0.7465 (mttt) cc_final: 0.6914 (tptt) REVERT: A 295 LEU cc_start: 0.7355 (tp) cc_final: 0.7086 (tt) REVERT: A 437 ASN cc_start: 0.8360 (t0) cc_final: 0.8005 (m-40) REVERT: A 451 LYS cc_start: 0.7360 (mmpt) cc_final: 0.7057 (mttt) REVERT: A 457 LYS cc_start: 0.6451 (pttt) cc_final: 0.6239 (tmtt) REVERT: A 458 LYS cc_start: 0.7104 (mmmt) cc_final: 0.6871 (mtmt) REVERT: B 96 ILE cc_start: 0.8397 (mt) cc_final: 0.8188 (mm) REVERT: B 182 ASP cc_start: 0.7269 (t70) cc_final: 0.6939 (t0) REVERT: B 275 LYS cc_start: 0.7466 (mttt) cc_final: 0.6918 (tptt) REVERT: B 295 LEU cc_start: 0.7380 (tp) cc_final: 0.7093 (tt) REVERT: B 437 ASN cc_start: 0.8357 (t0) cc_final: 0.8008 (m-40) REVERT: B 451 LYS cc_start: 0.7355 (mmpt) cc_final: 0.7046 (mttt) REVERT: B 458 LYS cc_start: 0.7244 (mmmt) cc_final: 0.6830 (ttmt) REVERT: C 96 ILE cc_start: 0.8371 (mt) cc_final: 0.8156 (mm) REVERT: C 182 ASP cc_start: 0.7342 (t70) cc_final: 0.7025 (t0) REVERT: C 275 LYS cc_start: 0.7500 (mttt) cc_final: 0.6877 (tptt) REVERT: C 295 LEU cc_start: 0.7340 (tp) cc_final: 0.7042 (tt) REVERT: C 437 ASN cc_start: 0.8357 (t0) cc_final: 0.8007 (m-40) REVERT: C 451 LYS cc_start: 0.7328 (mmpt) cc_final: 0.7076 (mttt) REVERT: C 457 LYS cc_start: 0.6449 (pttt) cc_final: 0.6234 (tmtt) REVERT: C 458 LYS cc_start: 0.7107 (mmmt) cc_final: 0.6856 (mtmt) REVERT: D 96 ILE cc_start: 0.8378 (mt) cc_final: 0.8166 (mm) REVERT: D 182 ASP cc_start: 0.7347 (t70) cc_final: 0.7030 (t0) REVERT: D 275 LYS cc_start: 0.7467 (mttt) cc_final: 0.6919 (tptt) REVERT: D 295 LEU cc_start: 0.7373 (tp) cc_final: 0.7075 (tt) REVERT: D 437 ASN cc_start: 0.8353 (t0) cc_final: 0.8005 (m-40) REVERT: D 451 LYS cc_start: 0.7314 (mmpt) cc_final: 0.7017 (mttt) REVERT: D 458 LYS cc_start: 0.7033 (mmmt) cc_final: 0.6822 (mtmt) outliers start: 24 outliers final: 12 residues processed: 180 average time/residue: 1.0161 time to fit residues: 203.3290 Evaluate side-chains 180 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 406 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.197023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139539 restraints weight = 14509.354| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.82 r_work: 0.2964 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13292 Z= 0.155 Angle : 0.556 6.929 18084 Z= 0.281 Chirality : 0.041 0.129 1992 Planarity : 0.005 0.046 2244 Dihedral : 4.978 44.772 1996 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.34 % Allowed : 10.91 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1552 helix: 1.28 (0.17), residues: 956 sheet: None (None), residues: 0 loop : -0.96 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 392 HIS 0.002 0.001 HIS D 60 PHE 0.024 0.002 PHE B 56 TYR 0.008 0.001 TYR B 365 ARG 0.002 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.06385 ( 687) hydrogen bonds : angle 4.55711 ( 2010) metal coordination : bond 0.00844 ( 16) metal coordination : angle 1.39592 ( 12) covalent geometry : bond 0.00365 (13276) covalent geometry : angle 0.55488 (18072) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 1.304 Fit side-chains REVERT: A 56 PHE cc_start: 0.8229 (t80) cc_final: 0.7634 (t80) REVERT: A 182 ASP cc_start: 0.7298 (t70) cc_final: 0.6905 (t70) REVERT: A 275 LYS cc_start: 0.7507 (mttt) cc_final: 0.6859 (tptt) REVERT: A 295 LEU cc_start: 0.7322 (tp) cc_final: 0.7092 (tt) REVERT: A 437 ASN cc_start: 0.8432 (t0) cc_final: 0.8126 (m110) REVERT: A 451 LYS cc_start: 0.7382 (mmpt) cc_final: 0.7110 (mttt) REVERT: A 457 LYS cc_start: 0.6480 (pttt) cc_final: 0.6252 (tmtt) REVERT: B 182 ASP cc_start: 0.7223 (t70) cc_final: 0.6883 (t70) REVERT: B 275 LYS cc_start: 0.7514 (mttt) cc_final: 0.6861 (tptt) REVERT: B 295 LEU cc_start: 0.7366 (tp) cc_final: 0.7109 (tt) REVERT: B 437 ASN cc_start: 0.8433 (t0) cc_final: 0.8132 (m110) REVERT: B 451 LYS cc_start: 0.7373 (mmpt) cc_final: 0.7053 (mttt) REVERT: B 458 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6868 (mtmt) REVERT: C 182 ASP cc_start: 0.7295 (t70) cc_final: 0.6900 (t70) REVERT: C 275 LYS cc_start: 0.7520 (mttt) cc_final: 0.6855 (tptt) REVERT: C 295 LEU cc_start: 0.7357 (tp) cc_final: 0.7083 (tt) REVERT: C 437 ASN cc_start: 0.8433 (t0) cc_final: 0.8133 (m110) REVERT: C 451 LYS cc_start: 0.7382 (mmpt) cc_final: 0.7110 (mttt) REVERT: C 457 LYS cc_start: 0.6464 (pttt) cc_final: 0.6232 (tmtt) REVERT: D 182 ASP cc_start: 0.7300 (t70) cc_final: 0.6911 (t70) REVERT: D 275 LYS cc_start: 0.7502 (mttt) cc_final: 0.6857 (tptt) REVERT: D 295 LEU cc_start: 0.7350 (tp) cc_final: 0.7109 (tt) REVERT: D 437 ASN cc_start: 0.8426 (t0) cc_final: 0.8131 (m110) REVERT: D 451 LYS cc_start: 0.7387 (mmpt) cc_final: 0.7074 (mttt) REVERT: D 458 LYS cc_start: 0.7087 (mmmt) cc_final: 0.6882 (mtmt) outliers start: 18 outliers final: 10 residues processed: 182 average time/residue: 1.2028 time to fit residues: 243.6651 Evaluate side-chains 178 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 406 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 24 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.197313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133514 restraints weight = 14468.411| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.78 r_work: 0.2970 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13292 Z= 0.147 Angle : 0.553 9.619 18084 Z= 0.277 Chirality : 0.041 0.129 1992 Planarity : 0.005 0.048 2244 Dihedral : 5.028 46.124 1996 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.63 % Allowed : 13.28 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1552 helix: 1.31 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 392 HIS 0.002 0.001 HIS A 383 PHE 0.026 0.001 PHE B 56 TYR 0.008 0.001 TYR C 365 ARG 0.002 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.06200 ( 687) hydrogen bonds : angle 4.42371 ( 2010) metal coordination : bond 0.00740 ( 16) metal coordination : angle 1.29923 ( 12) covalent geometry : bond 0.00347 (13276) covalent geometry : angle 0.55193 (18072) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.417 Fit side-chains REVERT: A 182 ASP cc_start: 0.7235 (t70) cc_final: 0.6829 (t70) REVERT: A 275 LYS cc_start: 0.7524 (mttt) cc_final: 0.6856 (tptt) REVERT: A 295 LEU cc_start: 0.7389 (tp) cc_final: 0.7176 (tt) REVERT: A 437 ASN cc_start: 0.8342 (t0) cc_final: 0.8017 (m110) REVERT: A 451 LYS cc_start: 0.7367 (mmpt) cc_final: 0.7108 (mttt) REVERT: A 457 LYS cc_start: 0.6390 (pttt) cc_final: 0.6167 (tmtt) REVERT: B 182 ASP cc_start: 0.7173 (t70) cc_final: 0.6823 (t70) REVERT: B 275 LYS cc_start: 0.7520 (mttt) cc_final: 0.6773 (tptp) REVERT: B 295 LEU cc_start: 0.7395 (tp) cc_final: 0.7191 (tt) REVERT: B 437 ASN cc_start: 0.8347 (t0) cc_final: 0.8022 (m110) REVERT: B 451 LYS cc_start: 0.7367 (mmpt) cc_final: 0.7101 (mttt) REVERT: B 458 LYS cc_start: 0.7089 (mmmt) cc_final: 0.6741 (mtmt) REVERT: C 182 ASP cc_start: 0.7228 (t70) cc_final: 0.6824 (t70) REVERT: C 213 GLU cc_start: 0.7489 (mp0) cc_final: 0.7274 (mp0) REVERT: C 275 LYS cc_start: 0.7525 (mttt) cc_final: 0.6760 (tptp) REVERT: C 295 LEU cc_start: 0.7391 (tp) cc_final: 0.7161 (tt) REVERT: C 437 ASN cc_start: 0.8329 (t0) cc_final: 0.8002 (m110) REVERT: C 451 LYS cc_start: 0.7347 (mmpt) cc_final: 0.7096 (mttt) REVERT: C 457 LYS cc_start: 0.6406 (pttt) cc_final: 0.6142 (tmtt) REVERT: D 182 ASP cc_start: 0.7233 (t70) cc_final: 0.6830 (t70) REVERT: D 275 LYS cc_start: 0.7523 (mttt) cc_final: 0.6855 (tptt) REVERT: D 295 LEU cc_start: 0.7393 (tp) cc_final: 0.7173 (tt) REVERT: D 437 ASN cc_start: 0.8342 (t0) cc_final: 0.8016 (m110) REVERT: D 451 LYS cc_start: 0.7372 (mmpt) cc_final: 0.7106 (mttt) REVERT: D 458 LYS cc_start: 0.7141 (mmmt) cc_final: 0.6810 (mtmt) outliers start: 22 outliers final: 14 residues processed: 180 average time/residue: 0.9660 time to fit residues: 194.2048 Evaluate side-chains 178 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 40 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.196335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130547 restraints weight = 14481.152| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.87 r_work: 0.2884 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13292 Z= 0.183 Angle : 0.582 7.781 18084 Z= 0.292 Chirality : 0.042 0.130 1992 Planarity : 0.005 0.049 2244 Dihedral : 5.335 51.419 1996 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.85 % Allowed : 12.76 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.22), residues: 1552 helix: 1.11 (0.17), residues: 968 sheet: None (None), residues: 0 loop : -1.11 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 392 HIS 0.003 0.001 HIS A 60 PHE 0.026 0.001 PHE A 56 TYR 0.009 0.001 TYR D 365 ARG 0.003 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.06935 ( 687) hydrogen bonds : angle 4.45603 ( 2010) metal coordination : bond 0.01009 ( 16) metal coordination : angle 1.49675 ( 12) covalent geometry : bond 0.00451 (13276) covalent geometry : angle 0.58082 (18072) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.450 Fit side-chains REVERT: A 182 ASP cc_start: 0.7289 (t70) cc_final: 0.6856 (t70) REVERT: A 275 LYS cc_start: 0.7560 (mttt) cc_final: 0.6791 (tptp) REVERT: A 295 LEU cc_start: 0.7281 (tp) cc_final: 0.7021 (tt) REVERT: A 437 ASN cc_start: 0.8354 (t0) cc_final: 0.7990 (m-40) REVERT: A 451 LYS cc_start: 0.7309 (mmpt) cc_final: 0.7017 (mttt) REVERT: A 457 LYS cc_start: 0.6381 (pttt) cc_final: 0.6086 (tmtt) REVERT: B 182 ASP cc_start: 0.7263 (t70) cc_final: 0.6884 (t70) REVERT: B 275 LYS cc_start: 0.7506 (mttt) cc_final: 0.6720 (tptp) REVERT: B 295 LEU cc_start: 0.7301 (tp) cc_final: 0.7049 (tt) REVERT: B 437 ASN cc_start: 0.8356 (t0) cc_final: 0.7996 (m-40) REVERT: B 451 LYS cc_start: 0.7309 (mmpt) cc_final: 0.7019 (mttt) REVERT: B 458 LYS cc_start: 0.7026 (mmmt) cc_final: 0.6688 (mtmt) REVERT: C 182 ASP cc_start: 0.7283 (t70) cc_final: 0.6850 (t70) REVERT: C 275 LYS cc_start: 0.7513 (mttt) cc_final: 0.6709 (tptp) REVERT: C 295 LEU cc_start: 0.7285 (tp) cc_final: 0.7016 (tt) REVERT: C 437 ASN cc_start: 0.8363 (t0) cc_final: 0.7936 (m-40) REVERT: C 451 LYS cc_start: 0.7283 (mmpt) cc_final: 0.7011 (mttt) REVERT: C 457 LYS cc_start: 0.6230 (pttt) cc_final: 0.6007 (tmtt) REVERT: D 182 ASP cc_start: 0.7283 (t70) cc_final: 0.6850 (t70) REVERT: D 275 LYS cc_start: 0.7559 (mttt) cc_final: 0.6792 (tptp) REVERT: D 295 LEU cc_start: 0.7293 (tp) cc_final: 0.7022 (tt) REVERT: D 437 ASN cc_start: 0.8352 (t0) cc_final: 0.7995 (m-40) REVERT: D 451 LYS cc_start: 0.7315 (mmpt) cc_final: 0.7020 (mttt) REVERT: D 458 LYS cc_start: 0.6988 (mmmt) cc_final: 0.6695 (mtmt) outliers start: 25 outliers final: 16 residues processed: 187 average time/residue: 0.8981 time to fit residues: 188.3664 Evaluate side-chains 180 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 94 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.198439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138426 restraints weight = 14627.114| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.92 r_work: 0.2930 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13292 Z= 0.135 Angle : 0.525 8.213 18084 Z= 0.265 Chirality : 0.040 0.130 1992 Planarity : 0.004 0.048 2244 Dihedral : 5.218 55.880 1996 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.56 % Allowed : 13.20 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1552 helix: 1.27 (0.17), residues: 964 sheet: None (None), residues: 0 loop : -1.02 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 392 HIS 0.002 0.001 HIS B 60 PHE 0.022 0.001 PHE A 56 TYR 0.007 0.001 TYR C 48 ARG 0.001 0.000 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.05849 ( 687) hydrogen bonds : angle 4.33113 ( 2010) metal coordination : bond 0.00696 ( 16) metal coordination : angle 1.15882 ( 12) covalent geometry : bond 0.00310 (13276) covalent geometry : angle 0.52461 (18072) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 1.420 Fit side-chains REVERT: A 182 ASP cc_start: 0.7373 (t70) cc_final: 0.6981 (t70) REVERT: A 275 LYS cc_start: 0.7613 (mttt) cc_final: 0.6866 (tptp) REVERT: A 295 LEU cc_start: 0.7289 (tp) cc_final: 0.7075 (tt) REVERT: A 437 ASN cc_start: 0.8589 (t0) cc_final: 0.8273 (m110) REVERT: A 451 LYS cc_start: 0.7354 (mmpt) cc_final: 0.7114 (mttt) REVERT: A 457 LYS cc_start: 0.6465 (pttt) cc_final: 0.6246 (tmtt) REVERT: B 182 ASP cc_start: 0.7361 (t70) cc_final: 0.6980 (t70) REVERT: B 275 LYS cc_start: 0.7618 (mttt) cc_final: 0.6852 (tptp) REVERT: B 437 ASN cc_start: 0.8589 (t0) cc_final: 0.8280 (m110) REVERT: B 451 LYS cc_start: 0.7351 (mmpt) cc_final: 0.7108 (mttt) REVERT: B 458 LYS cc_start: 0.7218 (mmmt) cc_final: 0.6928 (mtmt) REVERT: C 182 ASP cc_start: 0.7379 (t70) cc_final: 0.6983 (t70) REVERT: C 275 LYS cc_start: 0.7633 (mttt) cc_final: 0.6838 (tptp) REVERT: C 295 LEU cc_start: 0.7294 (tp) cc_final: 0.7064 (tt) REVERT: C 437 ASN cc_start: 0.8580 (t0) cc_final: 0.8275 (m110) REVERT: C 451 LYS cc_start: 0.7352 (mmpt) cc_final: 0.7113 (mttt) REVERT: D 182 ASP cc_start: 0.7376 (t70) cc_final: 0.6984 (t70) REVERT: D 265 ILE cc_start: 0.8150 (mt) cc_final: 0.7757 (pt) REVERT: D 275 LYS cc_start: 0.7600 (mttt) cc_final: 0.6856 (tptp) REVERT: D 295 LEU cc_start: 0.7317 (tp) cc_final: 0.7096 (tt) REVERT: D 437 ASN cc_start: 0.8594 (t0) cc_final: 0.8278 (m110) REVERT: D 451 LYS cc_start: 0.7364 (mmpt) cc_final: 0.7115 (mttt) REVERT: D 458 LYS cc_start: 0.7182 (mmmt) cc_final: 0.6915 (mtmt) outliers start: 21 outliers final: 17 residues processed: 179 average time/residue: 1.1837 time to fit residues: 237.5337 Evaluate side-chains 180 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.197497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138582 restraints weight = 14536.824| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.96 r_work: 0.2933 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13292 Z= 0.142 Angle : 0.552 16.418 18084 Z= 0.272 Chirality : 0.040 0.131 1992 Planarity : 0.004 0.048 2244 Dihedral : 5.265 58.845 1996 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.52 % Allowed : 12.98 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1552 helix: 1.29 (0.17), residues: 964 sheet: None (None), residues: 0 loop : -0.97 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 392 HIS 0.002 0.001 HIS B 60 PHE 0.012 0.001 PHE D 266 TYR 0.007 0.001 TYR B 48 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.05998 ( 687) hydrogen bonds : angle 4.31389 ( 2010) metal coordination : bond 0.00692 ( 16) metal coordination : angle 1.17016 ( 12) covalent geometry : bond 0.00331 (13276) covalent geometry : angle 0.55104 (18072) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.457 Fit side-chains REVERT: A 32 THR cc_start: 0.5866 (OUTLIER) cc_final: 0.5554 (p) REVERT: A 182 ASP cc_start: 0.7320 (t70) cc_final: 0.6939 (t70) REVERT: A 265 ILE cc_start: 0.8211 (mt) cc_final: 0.7817 (pt) REVERT: A 275 LYS cc_start: 0.7613 (mttt) cc_final: 0.6878 (tptp) REVERT: A 369 ILE cc_start: 0.7195 (mt) cc_final: 0.6959 (mt) REVERT: A 437 ASN cc_start: 0.8531 (t0) cc_final: 0.8207 (m110) REVERT: A 451 LYS cc_start: 0.7376 (mmpt) cc_final: 0.7143 (mttt) REVERT: A 457 LYS cc_start: 0.6439 (pttt) cc_final: 0.6228 (tmtt) REVERT: B 32 THR cc_start: 0.5929 (OUTLIER) cc_final: 0.5629 (p) REVERT: B 182 ASP cc_start: 0.7335 (t70) cc_final: 0.7011 (t70) REVERT: B 265 ILE cc_start: 0.8238 (mt) cc_final: 0.7810 (pt) REVERT: B 275 LYS cc_start: 0.7608 (mttt) cc_final: 0.6843 (tptp) REVERT: B 369 ILE cc_start: 0.7209 (mt) cc_final: 0.6971 (mt) REVERT: B 437 ASN cc_start: 0.8514 (t0) cc_final: 0.8191 (m110) REVERT: B 451 LYS cc_start: 0.7379 (mmpt) cc_final: 0.7135 (mttt) REVERT: B 458 LYS cc_start: 0.7210 (mmmt) cc_final: 0.6952 (mtmt) REVERT: C 32 THR cc_start: 0.5861 (OUTLIER) cc_final: 0.5563 (p) REVERT: C 182 ASP cc_start: 0.7327 (t70) cc_final: 0.6943 (t70) REVERT: C 265 ILE cc_start: 0.8207 (mt) cc_final: 0.7839 (pt) REVERT: C 275 LYS cc_start: 0.7602 (mttt) cc_final: 0.6861 (tptp) REVERT: C 295 LEU cc_start: 0.7343 (tp) cc_final: 0.7135 (tt) REVERT: C 437 ASN cc_start: 0.8526 (t0) cc_final: 0.8175 (m-40) REVERT: C 451 LYS cc_start: 0.7371 (mmpt) cc_final: 0.7138 (mttt) REVERT: D 32 THR cc_start: 0.5929 (OUTLIER) cc_final: 0.5633 (p) REVERT: D 182 ASP cc_start: 0.7325 (t70) cc_final: 0.6945 (t70) REVERT: D 265 ILE cc_start: 0.8204 (mt) cc_final: 0.7776 (pt) REVERT: D 275 LYS cc_start: 0.7607 (mttt) cc_final: 0.6874 (tptp) REVERT: D 369 ILE cc_start: 0.7233 (mt) cc_final: 0.7005 (mt) REVERT: D 437 ASN cc_start: 0.8535 (t0) cc_final: 0.8171 (m-40) REVERT: D 451 LYS cc_start: 0.7381 (mmpt) cc_final: 0.7142 (mttt) REVERT: D 458 LYS cc_start: 0.7167 (mmmt) cc_final: 0.6918 (mtmt) outliers start: 34 outliers final: 21 residues processed: 191 average time/residue: 0.8994 time to fit residues: 192.9149 Evaluate side-chains 183 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 126 optimal weight: 0.0050 chunk 83 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.198666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140115 restraints weight = 14558.499| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.97 r_work: 0.2942 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13292 Z= 0.126 Angle : 0.558 17.035 18084 Z= 0.268 Chirality : 0.039 0.155 1992 Planarity : 0.004 0.047 2244 Dihedral : 5.161 58.366 1996 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.93 % Allowed : 13.95 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1552 helix: 1.39 (0.17), residues: 964 sheet: None (None), residues: 0 loop : -0.90 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 392 HIS 0.002 0.001 HIS B 383 PHE 0.018 0.001 PHE A 56 TYR 0.007 0.001 TYR B 48 ARG 0.001 0.000 ARG C 314 Details of bonding type rmsd hydrogen bonds : bond 0.05503 ( 687) hydrogen bonds : angle 4.25830 ( 2010) metal coordination : bond 0.00597 ( 16) metal coordination : angle 1.03664 ( 12) covalent geometry : bond 0.00283 (13276) covalent geometry : angle 0.55754 (18072) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.435 Fit side-chains REVERT: A 32 THR cc_start: 0.5670 (OUTLIER) cc_final: 0.5365 (p) REVERT: A 182 ASP cc_start: 0.7305 (t70) cc_final: 0.6886 (t70) REVERT: A 265 ILE cc_start: 0.8124 (mt) cc_final: 0.7769 (pt) REVERT: A 275 LYS cc_start: 0.7606 (mttt) cc_final: 0.6842 (tptp) REVERT: A 437 ASN cc_start: 0.8557 (t0) cc_final: 0.8187 (m-40) REVERT: A 451 LYS cc_start: 0.7367 (mmpt) cc_final: 0.7109 (mttt) REVERT: B 32 THR cc_start: 0.5723 (OUTLIER) cc_final: 0.5431 (p) REVERT: B 182 ASP cc_start: 0.7328 (t70) cc_final: 0.6933 (t70) REVERT: B 265 ILE cc_start: 0.8193 (mt) cc_final: 0.7772 (pt) REVERT: B 275 LYS cc_start: 0.7613 (mttt) cc_final: 0.6851 (tptp) REVERT: B 437 ASN cc_start: 0.8527 (t0) cc_final: 0.8155 (m-40) REVERT: B 451 LYS cc_start: 0.7365 (mmpt) cc_final: 0.7097 (mttt) REVERT: B 458 LYS cc_start: 0.7156 (mmmt) cc_final: 0.6886 (mtmt) REVERT: C 32 THR cc_start: 0.5718 (OUTLIER) cc_final: 0.5406 (p) REVERT: C 182 ASP cc_start: 0.7305 (t70) cc_final: 0.6884 (t70) REVERT: C 265 ILE cc_start: 0.8108 (mt) cc_final: 0.7771 (pt) REVERT: C 275 LYS cc_start: 0.7602 (mttt) cc_final: 0.6830 (tptp) REVERT: C 437 ASN cc_start: 0.8533 (t0) cc_final: 0.8163 (m-40) REVERT: C 451 LYS cc_start: 0.7348 (mmpt) cc_final: 0.7095 (mttt) REVERT: D 32 THR cc_start: 0.5720 (OUTLIER) cc_final: 0.5425 (p) REVERT: D 182 ASP cc_start: 0.7332 (t70) cc_final: 0.6921 (t70) REVERT: D 265 ILE cc_start: 0.8142 (mt) cc_final: 0.7668 (pt) REVERT: D 275 LYS cc_start: 0.7606 (mttt) cc_final: 0.6838 (tptp) REVERT: D 437 ASN cc_start: 0.8568 (t0) cc_final: 0.8204 (m-40) REVERT: D 451 LYS cc_start: 0.7370 (mmpt) cc_final: 0.7096 (mttt) REVERT: D 458 LYS cc_start: 0.7144 (mmmt) cc_final: 0.6888 (mtmt) outliers start: 26 outliers final: 17 residues processed: 178 average time/residue: 0.9477 time to fit residues: 188.2436 Evaluate side-chains 177 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.195916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133639 restraints weight = 14479.552| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.70 r_work: 0.2958 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13292 Z= 0.185 Angle : 0.641 16.961 18084 Z= 0.305 Chirality : 0.043 0.150 1992 Planarity : 0.005 0.050 2244 Dihedral : 5.352 54.247 1996 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.15 % Allowed : 14.24 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1552 helix: 1.09 (0.17), residues: 988 sheet: 2.32 (0.89), residues: 40 loop : -1.17 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 392 HIS 0.003 0.001 HIS B 60 PHE 0.013 0.001 PHE A 384 TYR 0.009 0.001 TYR B 365 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.06938 ( 687) hydrogen bonds : angle 4.39995 ( 2010) metal coordination : bond 0.00946 ( 16) metal coordination : angle 1.30892 ( 12) covalent geometry : bond 0.00453 (13276) covalent geometry : angle 0.64072 (18072) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.426 Fit side-chains REVERT: A 32 THR cc_start: 0.5738 (OUTLIER) cc_final: 0.5444 (p) REVERT: A 182 ASP cc_start: 0.7231 (t70) cc_final: 0.6833 (t70) REVERT: A 265 ILE cc_start: 0.8128 (mt) cc_final: 0.7665 (pt) REVERT: A 275 LYS cc_start: 0.7596 (mttt) cc_final: 0.6848 (tptp) REVERT: A 369 ILE cc_start: 0.7153 (mt) cc_final: 0.6934 (mt) REVERT: A 437 ASN cc_start: 0.8362 (t0) cc_final: 0.8026 (m110) REVERT: A 451 LYS cc_start: 0.7360 (mmpt) cc_final: 0.7132 (mttt) REVERT: B 32 THR cc_start: 0.5774 (OUTLIER) cc_final: 0.5496 (p) REVERT: B 182 ASP cc_start: 0.7211 (t70) cc_final: 0.6882 (t70) REVERT: B 275 LYS cc_start: 0.7596 (mttt) cc_final: 0.6848 (tptp) REVERT: B 369 ILE cc_start: 0.7186 (mt) cc_final: 0.6967 (mt) REVERT: B 437 ASN cc_start: 0.8364 (t0) cc_final: 0.8031 (m110) REVERT: B 451 LYS cc_start: 0.7384 (mmpt) cc_final: 0.7135 (mttt) REVERT: B 458 LYS cc_start: 0.7117 (mmmt) cc_final: 0.6814 (mtmt) REVERT: C 32 THR cc_start: 0.5723 (OUTLIER) cc_final: 0.5448 (p) REVERT: C 182 ASP cc_start: 0.7232 (t70) cc_final: 0.6838 (t70) REVERT: C 265 ILE cc_start: 0.8101 (mt) cc_final: 0.7694 (pt) REVERT: C 275 LYS cc_start: 0.7617 (mttt) cc_final: 0.6860 (tptp) REVERT: C 369 ILE cc_start: 0.7182 (mt) cc_final: 0.6939 (mt) REVERT: C 437 ASN cc_start: 0.8354 (t0) cc_final: 0.8030 (m110) REVERT: C 451 LYS cc_start: 0.7361 (mmpt) cc_final: 0.7126 (mttt) REVERT: D 32 THR cc_start: 0.5765 (OUTLIER) cc_final: 0.5483 (p) REVERT: D 182 ASP cc_start: 0.7234 (t70) cc_final: 0.6834 (t70) REVERT: D 275 LYS cc_start: 0.7593 (mttt) cc_final: 0.6848 (tptp) REVERT: D 369 ILE cc_start: 0.7192 (mt) cc_final: 0.6985 (mt) REVERT: D 437 ASN cc_start: 0.8360 (t0) cc_final: 0.8031 (m-40) REVERT: D 451 LYS cc_start: 0.7359 (mmpt) cc_final: 0.7120 (mttt) REVERT: D 458 LYS cc_start: 0.7136 (mmmt) cc_final: 0.6797 (mtmt) outliers start: 29 outliers final: 17 residues processed: 181 average time/residue: 1.1100 time to fit residues: 222.6460 Evaluate side-chains 176 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 114 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 128 optimal weight: 0.0870 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.199810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135184 restraints weight = 14425.958| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.75 r_work: 0.3020 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13292 Z= 0.119 Angle : 0.565 16.085 18084 Z= 0.270 Chirality : 0.039 0.158 1992 Planarity : 0.004 0.047 2244 Dihedral : 4.936 58.920 1996 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.41 % Allowed : 15.43 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1552 helix: 1.29 (0.17), residues: 984 sheet: 2.43 (0.93), residues: 40 loop : -1.05 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 392 HIS 0.002 0.000 HIS D 60 PHE 0.017 0.001 PHE B 56 TYR 0.007 0.001 TYR A 48 ARG 0.002 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.05250 ( 687) hydrogen bonds : angle 4.25290 ( 2010) metal coordination : bond 0.00557 ( 16) metal coordination : angle 0.90484 ( 12) covalent geometry : bond 0.00260 (13276) covalent geometry : angle 0.56428 (18072) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.681 Fit side-chains REVERT: A 32 THR cc_start: 0.5815 (OUTLIER) cc_final: 0.5487 (p) REVERT: A 182 ASP cc_start: 0.7183 (t70) cc_final: 0.6802 (t70) REVERT: A 265 ILE cc_start: 0.8116 (mt) cc_final: 0.7749 (pt) REVERT: A 275 LYS cc_start: 0.7601 (mttt) cc_final: 0.6860 (tptp) REVERT: A 369 ILE cc_start: 0.7072 (mt) cc_final: 0.6857 (mt) REVERT: A 437 ASN cc_start: 0.8361 (t0) cc_final: 0.7975 (m-40) REVERT: A 451 LYS cc_start: 0.7360 (mmpt) cc_final: 0.7135 (mttt) REVERT: B 32 THR cc_start: 0.5784 (OUTLIER) cc_final: 0.5482 (p) REVERT: B 182 ASP cc_start: 0.7175 (t70) cc_final: 0.6818 (t70) REVERT: B 265 ILE cc_start: 0.8193 (mt) cc_final: 0.7767 (pt) REVERT: B 275 LYS cc_start: 0.7609 (mttt) cc_final: 0.6876 (tptp) REVERT: B 369 ILE cc_start: 0.7079 (mt) cc_final: 0.6861 (mt) REVERT: B 437 ASN cc_start: 0.8368 (t0) cc_final: 0.7977 (m-40) REVERT: B 451 LYS cc_start: 0.7392 (mmpt) cc_final: 0.7144 (mttt) REVERT: B 458 LYS cc_start: 0.7197 (mmmt) cc_final: 0.6877 (mtmt) REVERT: C 32 THR cc_start: 0.5766 (OUTLIER) cc_final: 0.5461 (p) REVERT: C 182 ASP cc_start: 0.7192 (t70) cc_final: 0.6809 (t70) REVERT: C 265 ILE cc_start: 0.8096 (mt) cc_final: 0.7754 (pt) REVERT: C 275 LYS cc_start: 0.7625 (mttt) cc_final: 0.6876 (tptp) REVERT: C 437 ASN cc_start: 0.8351 (t0) cc_final: 0.7967 (m-40) REVERT: C 451 LYS cc_start: 0.7371 (mmpt) cc_final: 0.7146 (mttt) REVERT: D 32 THR cc_start: 0.5781 (OUTLIER) cc_final: 0.5476 (p) REVERT: D 182 ASP cc_start: 0.7189 (t70) cc_final: 0.6804 (t70) REVERT: D 265 ILE cc_start: 0.8170 (mt) cc_final: 0.7729 (pt) REVERT: D 275 LYS cc_start: 0.7593 (mttt) cc_final: 0.6860 (tptp) REVERT: D 369 ILE cc_start: 0.7090 (mt) cc_final: 0.6873 (mt) REVERT: D 437 ASN cc_start: 0.8358 (t0) cc_final: 0.7971 (m-40) REVERT: D 451 LYS cc_start: 0.7395 (mmpt) cc_final: 0.7143 (mttt) REVERT: D 458 LYS cc_start: 0.7199 (mmmt) cc_final: 0.6904 (mtmt) outliers start: 19 outliers final: 12 residues processed: 167 average time/residue: 1.2606 time to fit residues: 235.0316 Evaluate side-chains 166 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 92 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.196301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135396 restraints weight = 14289.003| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.97 r_work: 0.2902 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13292 Z= 0.197 Angle : 0.649 16.306 18084 Z= 0.311 Chirality : 0.043 0.152 1992 Planarity : 0.005 0.050 2244 Dihedral : 5.122 57.345 1996 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.41 % Allowed : 15.43 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1552 helix: 1.08 (0.17), residues: 988 sheet: 2.38 (0.90), residues: 40 loop : -1.20 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 392 HIS 0.003 0.001 HIS C 383 PHE 0.017 0.001 PHE D 266 TYR 0.010 0.001 TYR D 365 ARG 0.003 0.000 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.07088 ( 687) hydrogen bonds : angle 4.40954 ( 2010) metal coordination : bond 0.00953 ( 16) metal coordination : angle 1.26577 ( 12) covalent geometry : bond 0.00489 (13276) covalent geometry : angle 0.64845 (18072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9796.08 seconds wall clock time: 173 minutes 57.67 seconds (10437.67 seconds total)