Starting phenix.real_space_refine on Fri Jul 3 08:14:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f1d_28795/07_2026/8f1d_28795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f1d_28795/07_2026/8f1d_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_2026/8f1d_28795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f1d_28795/07_2026/8f1d_28795.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8f1d_28795/07_2026/8f1d_28795.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f1d_28795/07_2026/8f1d_28795.cif" model { file = "/net/cci-nas-00/data/ceres_data/8f1d_28795/07_2026/8f1d_28795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f1d_28795/07_2026/8f1d_28795.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.88, per 1000 atoms: 0.22 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: 1.07 Conformation dependent library (CDL) restraints added in 465.9 milliseconds 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: 0.35 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: 2.05 Time building geometry restraints manager: 1.34 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: 7192 16.27 - 32.53: 407 32.53 - 48.80: 73 48.80 - 65.07: 8 65.07 - 81.33: 4 Dihedral angle restraints: 7684 sinusoidal: 3076 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 7681 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 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: 1.920 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.410 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 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 : 10.466 81.332 4708 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (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 ARG 0.002 0.000 ARG C 320 TYR 0.008 0.001 TYR B 365 PHE 0.007 0.001 PHE D 244 TRP 0.008 0.001 TRP B 392 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (13276) covalent geometry : angle 0.50907 / 0.26 (18072) hydrogen bonds : bond 0.16980 / 11.60 ( 687) hydrogen bonds : angle 5.64301 / 4.02 ( 2010) metal coordination : bond 0.01222 / 0.70 ( 16) metal coordination : angle 1.15211 / 0.67 ( 12) *********************** 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 : 0.496 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: 0.6503 (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: 0.7155 (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: 0.4901 time to fit residues: 124.2657 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 : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.198775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136027 restraints weight = 14595.742| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.94 r_work: 0.2985 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1309 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 : 0.547 9.052 18084 Z= 0.275 Chirality : 0.041 0.141 1992 Planarity : 0.004 0.043 2244 Dihedral : 4.062 40.042 1772 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.96 % Allowed : 9.87 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.22), residues: 1552 helix: 1.63 (0.18), residues: 956 sheet: None (None), residues: 0 loop : -0.74 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 110 TYR 0.009 0.001 TYR C 365 PHE 0.017 0.001 PHE D 56 TRP 0.010 0.001 TRP D 392 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (13276) covalent geometry : angle 0.54498 / 0.27 (18072) hydrogen bonds : bond 0.05899 / 3.98 ( 687) hydrogen bonds : angle 4.57851 / 3.27 ( 2010) metal coordination : bond 0.01170 / 0.67 ( 16) metal coordination : angle 2.10617 / 1.17 ( 12) *********************** 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: 13 poor density : 181 time to evaluate : 0.500 Fit side-chains REVERT: A 182 ASP cc_start: 0.7319 (t0) cc_final: 0.7001 (t0) REVERT: A 275 LYS cc_start: 0.7445 (mttt) cc_final: 0.6910 (tptt) REVERT: A 437 ASN cc_start: 0.8349 (t0) cc_final: 0.7970 (m110) REVERT: A 451 LYS cc_start: 0.7345 (mmpt) cc_final: 0.7026 (mttt) REVERT: A 457 LYS cc_start: 0.6455 (pttt) cc_final: 0.6219 (tptm) REVERT: A 458 LYS cc_start: 0.7062 (mmmt) cc_final: 0.6833 (mtmt) REVERT: B 182 ASP cc_start: 0.7265 (t70) cc_final: 0.6932 (t0) REVERT: B 213 GLU cc_start: 0.7437 (mp0) cc_final: 0.7223 (mp0) REVERT: B 275 LYS cc_start: 0.7449 (mttt) cc_final: 0.6913 (tptt) REVERT: B 437 ASN cc_start: 0.8349 (t0) cc_final: 0.7969 (m110) REVERT: B 451 LYS cc_start: 0.7317 (mmpt) cc_final: 0.7005 (mttt) REVERT: B 458 LYS cc_start: 0.7133 (mmmt) cc_final: 0.6746 (ttmt) REVERT: C 182 ASP cc_start: 0.7322 (t0) cc_final: 0.7001 (t0) REVERT: C 213 GLU cc_start: 0.7425 (mp0) cc_final: 0.7214 (mp0) REVERT: C 275 LYS cc_start: 0.7457 (mttt) cc_final: 0.6907 (tptt) REVERT: C 437 ASN cc_start: 0.8355 (t0) cc_final: 0.7981 (m110) REVERT: C 451 LYS cc_start: 0.7345 (mmpt) cc_final: 0.7029 (mttt) REVERT: C 457 LYS cc_start: 0.6424 (pttt) cc_final: 0.6180 (tmtt) REVERT: C 458 LYS cc_start: 0.7091 (mmmt) cc_final: 0.6842 (mtmt) REVERT: D 182 ASP cc_start: 0.7318 (t0) cc_final: 0.6995 (t0) REVERT: D 275 LYS cc_start: 0.7449 (mttt) cc_final: 0.6916 (tptt) REVERT: D 437 ASN cc_start: 0.8329 (t0) cc_final: 0.7967 (m110) REVERT: D 451 LYS cc_start: 0.7364 (mmpt) cc_final: 0.7051 (mttt) REVERT: D 457 LYS cc_start: 0.6353 (pttt) cc_final: 0.6127 (tptm) REVERT: D 458 LYS cc_start: 0.7058 (mmmt) cc_final: 0.6845 (mtmt) outliers start: 13 outliers final: 10 residues processed: 186 average time/residue: 0.4469 time to fit residues: 91.9985 Evaluate side-chains 181 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 55 optimal weight: 0.0010 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 9 optimal weight: 0.0050 chunk 104 optimal weight: 5.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.199331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139615 restraints weight = 14733.758| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.89 r_work: 0.2982 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1673 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= 0.129 Angle : 0.562 14.384 18084 Z= 0.271 Chirality : 0.040 0.143 1992 Planarity : 0.004 0.044 2244 Dihedral : 4.015 38.832 1772 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.26 % Allowed : 9.79 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.22), residues: 1552 helix: 1.60 (0.17), residues: 956 sheet: None (None), residues: 0 loop : -0.84 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 110 TYR 0.008 0.001 TYR B 365 PHE 0.024 0.001 PHE B 56 TRP 0.010 0.001 TRP A 392 HIS 0.002 0.001 HIS C 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (13276) covalent geometry : angle 0.56135 / 0.27 (18072) hydrogen bonds : bond 0.05630 / 3.80 ( 687) hydrogen bonds : angle 4.39043 / 3.13 ( 2010) metal coordination : bond 0.00626 / 0.36 ( 16) metal coordination : angle 1.25003 / 0.69 ( 12) *********************** 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 198 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.320 Fit side-chains REVERT: A 182 ASP cc_start: 0.7366 (t70) cc_final: 0.7006 (t70) REVERT: A 275 LYS cc_start: 0.7532 (mttt) cc_final: 0.6882 (tptt) REVERT: A 437 ASN cc_start: 0.8536 (t0) cc_final: 0.8176 (m-40) REVERT: A 451 LYS cc_start: 0.7357 (mmpt) cc_final: 0.7040 (mttt) REVERT: A 457 LYS cc_start: 0.6462 (pttt) cc_final: 0.6253 (tptm) REVERT: B 182 ASP cc_start: 0.7346 (t70) cc_final: 0.7039 (t0) REVERT: B 275 LYS cc_start: 0.7535 (mttt) cc_final: 0.6893 (tptt) REVERT: B 437 ASN cc_start: 0.8530 (t0) cc_final: 0.8176 (m-40) REVERT: B 451 LYS cc_start: 0.7323 (mmpt) cc_final: 0.7017 (mttt) REVERT: B 458 LYS cc_start: 0.7217 (mmmt) cc_final: 0.6914 (mtmt) REVERT: C 182 ASP cc_start: 0.7391 (t70) cc_final: 0.7033 (t70) REVERT: C 275 LYS cc_start: 0.7561 (mttt) cc_final: 0.6895 (tptt) REVERT: C 437 ASN cc_start: 0.8517 (t0) cc_final: 0.8169 (m-40) REVERT: C 451 LYS cc_start: 0.7354 (mmpt) cc_final: 0.7051 (mttt) REVERT: D 182 ASP cc_start: 0.7373 (t70) cc_final: 0.7013 (t70) REVERT: D 275 LYS cc_start: 0.7526 (mttt) cc_final: 0.6881 (tptt) REVERT: D 437 ASN cc_start: 0.8522 (t0) cc_final: 0.8168 (m110) REVERT: D 451 LYS cc_start: 0.7362 (mmpt) cc_final: 0.7053 (mttt) REVERT: D 457 LYS cc_start: 0.6467 (pttt) cc_final: 0.6239 (tptm) outliers start: 17 outliers final: 8 residues processed: 188 average time/residue: 0.4354 time to fit residues: 91.1626 Evaluate side-chains 182 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain D residue 253 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 16 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4196 r_free = 0.4196 target = 0.196435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139664 restraints weight = 14614.048| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.84 r_work: 0.2945 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13292 Z= 0.186 Angle : 0.636 14.360 18084 Z= 0.304 Chirality : 0.043 0.136 1992 Planarity : 0.005 0.049 2244 Dihedral : 4.396 44.054 1772 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.56 % Allowed : 13.13 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.22), residues: 1552 helix: 1.35 (0.17), residues: 960 sheet: 2.72 (0.89), residues: 40 loop : -1.09 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.012 0.001 TYR C 365 PHE 0.026 0.002 PHE B 56 TRP 0.010 0.001 TRP C 392 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (13276) covalent geometry : angle 0.63531 / 0.30 (18072) hydrogen bonds : bond 0.06883 / 4.65 ( 687) hydrogen bonds : angle 4.46039 / 3.17 ( 2010) metal coordination : bond 0.00917 / 0.52 ( 16) metal coordination : angle 1.59463 / 0.89 ( 12) *********************** 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 199 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.395 Fit side-chains REVERT: A 182 ASP cc_start: 0.7358 (t70) cc_final: 0.7006 (t70) REVERT: A 275 LYS cc_start: 0.7572 (mttt) cc_final: 0.6939 (tptt) REVERT: A 437 ASN cc_start: 0.8497 (t0) cc_final: 0.8175 (m-40) REVERT: A 451 LYS cc_start: 0.7350 (mmpt) cc_final: 0.7048 (mttt) REVERT: B 182 ASP cc_start: 0.7280 (t70) cc_final: 0.6987 (t0) REVERT: B 275 LYS cc_start: 0.7574 (mttt) cc_final: 0.6938 (tptt) REVERT: B 437 ASN cc_start: 0.8499 (t0) cc_final: 0.8182 (m-40) REVERT: B 451 LYS cc_start: 0.7337 (mmpt) cc_final: 0.7028 (mttt) REVERT: B 458 LYS cc_start: 0.7174 (mmmt) cc_final: 0.6820 (ttmt) REVERT: C 96 ILE cc_start: 0.8533 (mt) cc_final: 0.8331 (mm) REVERT: C 182 ASP cc_start: 0.7362 (t70) cc_final: 0.7008 (t70) REVERT: C 275 LYS cc_start: 0.7564 (mttt) cc_final: 0.6887 (tptt) REVERT: C 437 ASN cc_start: 0.8492 (t0) cc_final: 0.8180 (m-40) REVERT: C 451 LYS cc_start: 0.7316 (mmpt) cc_final: 0.7043 (mttt) REVERT: D 96 ILE cc_start: 0.8527 (mt) cc_final: 0.8325 (mm) REVERT: D 182 ASP cc_start: 0.7358 (t70) cc_final: 0.7009 (t70) REVERT: D 275 LYS cc_start: 0.7564 (mttt) cc_final: 0.6896 (tptt) REVERT: D 437 ASN cc_start: 0.8495 (t0) cc_final: 0.8181 (m-40) REVERT: D 451 LYS cc_start: 0.7321 (mmpt) cc_final: 0.7041 (mttt) outliers start: 21 outliers final: 11 residues processed: 185 average time/residue: 0.4452 time to fit residues: 91.4487 Evaluate side-chains 187 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 406 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 84 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.195546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130154 restraints weight = 14554.561| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.84 r_work: 0.2902 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13292 Z= 0.208 Angle : 0.653 14.752 18084 Z= 0.315 Chirality : 0.044 0.140 1992 Planarity : 0.005 0.051 2244 Dihedral : 5.083 52.935 1772 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.08 % Allowed : 12.39 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1552 helix: 1.11 (0.17), residues: 964 sheet: 2.60 (0.87), residues: 40 loop : -1.24 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 33 TYR 0.011 0.002 TYR C 365 PHE 0.022 0.002 PHE A 56 TRP 0.012 0.002 TRP D 392 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (13276) covalent geometry : angle 0.65186 / 0.32 (18072) hydrogen bonds : bond 0.07316 / 4.95 ( 687) hydrogen bonds : angle 4.52518 / 3.22 ( 2010) metal coordination : bond 0.01113 / 0.63 ( 16) metal coordination : angle 1.62498 / 0.90 ( 12) *********************** 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 204 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.489 Fit side-chains REVERT: A 56 PHE cc_start: 0.7826 (t80) cc_final: 0.7470 (t80) REVERT: A 182 ASP cc_start: 0.7279 (t70) cc_final: 0.6840 (t70) REVERT: A 275 LYS cc_start: 0.7522 (mttt) cc_final: 0.6760 (tptp) REVERT: A 437 ASN cc_start: 0.8340 (t0) cc_final: 0.7930 (m110) REVERT: A 451 LYS cc_start: 0.7308 (mmpt) cc_final: 0.7016 (mttt) REVERT: B 182 ASP cc_start: 0.7258 (t70) cc_final: 0.6901 (t0) REVERT: B 275 LYS cc_start: 0.7523 (mttt) cc_final: 0.6764 (tptp) REVERT: B 437 ASN cc_start: 0.8346 (t0) cc_final: 0.7940 (m110) REVERT: B 451 LYS cc_start: 0.7249 (mmpt) cc_final: 0.6972 (mttt) REVERT: B 458 LYS cc_start: 0.7030 (mmmt) cc_final: 0.6674 (mtmt) REVERT: C 182 ASP cc_start: 0.7278 (t70) cc_final: 0.6839 (t70) REVERT: C 275 LYS cc_start: 0.7523 (mttt) cc_final: 0.6713 (tptp) REVERT: C 437 ASN cc_start: 0.8339 (t0) cc_final: 0.7939 (m110) REVERT: C 451 LYS cc_start: 0.7275 (mmpt) cc_final: 0.7001 (mttt) REVERT: D 182 ASP cc_start: 0.7278 (t70) cc_final: 0.6842 (t70) REVERT: D 275 LYS cc_start: 0.7510 (mttt) cc_final: 0.6750 (tptp) REVERT: D 437 ASN cc_start: 0.8367 (t0) cc_final: 0.7971 (m110) REVERT: D 451 LYS cc_start: 0.7272 (mmpt) cc_final: 0.6960 (mttt) outliers start: 28 outliers final: 16 residues processed: 192 average time/residue: 0.4213 time to fit residues: 90.3274 Evaluate side-chains 189 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 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 251 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 251 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 251 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.198161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138864 restraints weight = 14473.138| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.89 r_work: 0.2958 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2319 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 : 0.561 14.714 18084 Z= 0.269 Chirality : 0.039 0.138 1992 Planarity : 0.004 0.048 2244 Dihedral : 5.003 56.480 1772 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.74 % Allowed : 13.80 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1552 helix: 1.34 (0.17), residues: 960 sheet: 2.76 (0.89), residues: 40 loop : -1.12 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 314 TYR 0.006 0.001 TYR B 48 PHE 0.018 0.001 PHE D 56 TRP 0.011 0.001 TRP A 392 HIS 0.002 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (13276) covalent geometry : angle 0.56049 / 0.27 (18072) hydrogen bonds : bond 0.05561 / 3.76 ( 687) hydrogen bonds : angle 4.32693 / 3.07 ( 2010) metal coordination : bond 0.00672 / 0.39 ( 16) metal coordination : angle 1.09003 / 0.61 ( 12) *********************** 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 176 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.495 Fit side-chains REVERT: A 116 GLU cc_start: 0.7236 (tp30) cc_final: 0.6683 (pt0) REVERT: A 182 ASP cc_start: 0.7349 (t70) cc_final: 0.6942 (t70) REVERT: A 265 ILE cc_start: 0.8095 (mt) cc_final: 0.7679 (pt) REVERT: A 275 LYS cc_start: 0.7597 (mttt) cc_final: 0.6837 (tptp) REVERT: A 437 ASN cc_start: 0.8526 (t0) cc_final: 0.8206 (m110) REVERT: A 451 LYS cc_start: 0.7352 (mmpt) cc_final: 0.7090 (mttt) REVERT: B 182 ASP cc_start: 0.7341 (t70) cc_final: 0.7004 (t70) REVERT: B 265 ILE cc_start: 0.8091 (mt) cc_final: 0.7678 (pt) REVERT: B 275 LYS cc_start: 0.7598 (mttt) cc_final: 0.6844 (tptp) REVERT: B 437 ASN cc_start: 0.8518 (t0) cc_final: 0.8209 (m110) REVERT: B 451 LYS cc_start: 0.7341 (mmpt) cc_final: 0.7072 (mttt) REVERT: B 458 LYS cc_start: 0.7192 (mmmt) cc_final: 0.6873 (mtmt) REVERT: C 182 ASP cc_start: 0.7350 (t70) cc_final: 0.6944 (t70) REVERT: C 265 ILE cc_start: 0.8103 (mt) cc_final: 0.7682 (pt) REVERT: C 275 LYS cc_start: 0.7578 (mttt) cc_final: 0.6822 (tptp) REVERT: C 437 ASN cc_start: 0.8517 (t0) cc_final: 0.8210 (m110) REVERT: C 451 LYS cc_start: 0.7361 (mmpt) cc_final: 0.7093 (mttt) REVERT: D 182 ASP cc_start: 0.7391 (t70) cc_final: 0.6988 (t70) REVERT: D 265 ILE cc_start: 0.8071 (mt) cc_final: 0.7647 (pt) REVERT: D 275 LYS cc_start: 0.7596 (mttt) cc_final: 0.6834 (tptp) REVERT: D 437 ASN cc_start: 0.8530 (t0) cc_final: 0.8211 (m110) REVERT: D 451 LYS cc_start: 0.7388 (mmpt) cc_final: 0.7079 (mttt) outliers start: 10 outliers final: 8 residues processed: 171 average time/residue: 0.4261 time to fit residues: 81.0221 Evaluate side-chains 174 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 166 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 77 optimal weight: 0.0370 chunk 102 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.198338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139737 restraints weight = 14553.906| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.87 r_work: 0.2980 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2405 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= 0.127 Angle : 0.566 15.072 18084 Z= 0.269 Chirality : 0.040 0.143 1992 Planarity : 0.004 0.048 2244 Dihedral : 5.055 59.476 1772 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.48 % Allowed : 13.58 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.22), residues: 1552 helix: 1.42 (0.17), residues: 960 sheet: 2.82 (0.91), residues: 40 loop : -1.06 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 33 TYR 0.007 0.001 TYR D 365 PHE 0.013 0.001 PHE A 266 TRP 0.010 0.001 TRP B 392 HIS 0.002 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (13276) covalent geometry : angle 0.56559 / 0.27 (18072) hydrogen bonds : bond 0.05569 / 3.77 ( 687) hydrogen bonds : angle 4.27522 / 3.03 ( 2010) metal coordination : bond 0.00600 / 0.34 ( 16) metal coordination : angle 1.08115 / 0.61 ( 12) *********************** 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 188 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.481 Fit side-chains REVERT: A 32 THR cc_start: 0.5761 (OUTLIER) cc_final: 0.5454 (p) REVERT: A 182 ASP cc_start: 0.7331 (t70) cc_final: 0.6934 (t70) REVERT: A 265 ILE cc_start: 0.8193 (mt) cc_final: 0.7739 (pt) REVERT: A 275 LYS cc_start: 0.7619 (mttt) cc_final: 0.6878 (tptp) REVERT: A 437 ASN cc_start: 0.8515 (t0) cc_final: 0.8166 (m110) REVERT: A 451 LYS cc_start: 0.7399 (mmpt) cc_final: 0.7139 (mttt) REVERT: B 32 THR cc_start: 0.5799 (OUTLIER) cc_final: 0.5506 (p) REVERT: B 182 ASP cc_start: 0.7316 (t70) cc_final: 0.6990 (t70) REVERT: B 265 ILE cc_start: 0.8215 (mt) cc_final: 0.7794 (pt) REVERT: B 275 LYS cc_start: 0.7619 (mttt) cc_final: 0.6883 (tptp) REVERT: B 437 ASN cc_start: 0.8514 (t0) cc_final: 0.8169 (m110) REVERT: B 451 LYS cc_start: 0.7364 (mmpt) cc_final: 0.7107 (mttt) REVERT: B 458 LYS cc_start: 0.7203 (mmmt) cc_final: 0.6927 (mtmt) REVERT: C 32 THR cc_start: 0.5742 (OUTLIER) cc_final: 0.5450 (p) REVERT: C 182 ASP cc_start: 0.7333 (t70) cc_final: 0.6948 (t70) REVERT: C 265 ILE cc_start: 0.8140 (mt) cc_final: 0.7616 (pt) REVERT: C 275 LYS cc_start: 0.7602 (mttt) cc_final: 0.6861 (tptp) REVERT: C 437 ASN cc_start: 0.8502 (t0) cc_final: 0.8160 (m110) REVERT: C 451 LYS cc_start: 0.7380 (mmpt) cc_final: 0.7125 (mttt) REVERT: D 32 THR cc_start: 0.5784 (OUTLIER) cc_final: 0.5492 (p) REVERT: D 182 ASP cc_start: 0.7340 (t70) cc_final: 0.6945 (t70) REVERT: D 265 ILE cc_start: 0.8191 (mt) cc_final: 0.7738 (pt) REVERT: D 275 LYS cc_start: 0.7607 (mttt) cc_final: 0.6870 (tptp) REVERT: D 437 ASN cc_start: 0.8512 (t0) cc_final: 0.8168 (m110) REVERT: D 451 LYS cc_start: 0.7376 (mmpt) cc_final: 0.7121 (mttt) outliers start: 20 outliers final: 12 residues processed: 183 average time/residue: 0.4175 time to fit residues: 85.1346 Evaluate side-chains 174 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 253 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 D residue 32 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 100 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.196973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134056 restraints weight = 14375.261| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.99 r_work: 0.2954 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2461 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= 0.159 Angle : 0.593 14.726 18084 Z= 0.285 Chirality : 0.041 0.136 1992 Planarity : 0.005 0.049 2244 Dihedral : 5.283 59.685 1772 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.63 % Allowed : 13.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1552 helix: 1.30 (0.17), residues: 960 sheet: 2.72 (0.90), residues: 40 loop : -1.08 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 33 TYR 0.009 0.001 TYR C 365 PHE 0.020 0.001 PHE A 56 TRP 0.011 0.001 TRP D 392 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (13276) covalent geometry : angle 0.59212 / 0.28 (18072) hydrogen bonds : bond 0.06409 / 4.33 ( 687) hydrogen bonds : angle 4.33006 / 3.07 ( 2010) metal coordination : bond 0.00787 / 0.46 ( 16) metal coordination : angle 1.23114 / 0.69 ( 12) *********************** 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 177 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.436 Fit side-chains REVERT: A 32 THR cc_start: 0.5692 (OUTLIER) cc_final: 0.5394 (p) REVERT: A 182 ASP cc_start: 0.7238 (t70) cc_final: 0.6835 (t70) REVERT: A 275 LYS cc_start: 0.7594 (mttt) cc_final: 0.6828 (tptp) REVERT: A 437 ASN cc_start: 0.8390 (t0) cc_final: 0.8045 (m110) REVERT: A 451 LYS cc_start: 0.7366 (mmpt) cc_final: 0.7115 (mttt) REVERT: B 32 THR cc_start: 0.5799 (OUTLIER) cc_final: 0.5512 (p) REVERT: B 182 ASP cc_start: 0.7260 (t70) cc_final: 0.6924 (t70) REVERT: B 275 LYS cc_start: 0.7582 (mttt) cc_final: 0.6847 (tptp) REVERT: B 437 ASN cc_start: 0.8384 (t0) cc_final: 0.8046 (m110) REVERT: B 451 LYS cc_start: 0.7348 (mmpt) cc_final: 0.7104 (mttt) REVERT: B 458 LYS cc_start: 0.7118 (mmmt) cc_final: 0.6861 (mtmt) REVERT: C 32 THR cc_start: 0.5743 (OUTLIER) cc_final: 0.5463 (p) REVERT: C 182 ASP cc_start: 0.7235 (t70) cc_final: 0.6840 (t70) REVERT: C 275 LYS cc_start: 0.7580 (mttt) cc_final: 0.6833 (tptp) REVERT: C 437 ASN cc_start: 0.8380 (t0) cc_final: 0.8047 (m110) REVERT: C 451 LYS cc_start: 0.7358 (mmpt) cc_final: 0.7104 (mttt) REVERT: D 32 THR cc_start: 0.5766 (OUTLIER) cc_final: 0.5491 (p) REVERT: D 182 ASP cc_start: 0.7239 (t70) cc_final: 0.6834 (t70) REVERT: D 275 LYS cc_start: 0.7575 (mttt) cc_final: 0.6836 (tptp) REVERT: D 437 ASN cc_start: 0.8394 (t0) cc_final: 0.8054 (m110) REVERT: D 451 LYS cc_start: 0.7357 (mmpt) cc_final: 0.7108 (mttt) outliers start: 22 outliers final: 14 residues processed: 172 average time/residue: 0.4110 time to fit residues: 78.9571 Evaluate side-chains 173 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 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 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 13 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.198275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141484 restraints weight = 14569.777| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.91 r_work: 0.2988 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2518 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= 0.133 Angle : 0.567 14.619 18084 Z= 0.273 Chirality : 0.040 0.136 1992 Planarity : 0.004 0.048 2244 Dihedral : 5.240 59.791 1772 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.56 % Allowed : 14.76 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.22), residues: 1552 helix: 1.37 (0.17), residues: 960 sheet: 2.79 (0.91), residues: 40 loop : -1.04 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 110 TYR 0.007 0.001 TYR D 365 PHE 0.011 0.001 PHE D 266 TRP 0.010 0.001 TRP C 392 HIS 0.002 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (13276) covalent geometry : angle 0.56658 / 0.27 (18072) hydrogen bonds : bond 0.05708 / 3.86 ( 687) hydrogen bonds : angle 4.27180 / 3.03 ( 2010) metal coordination : bond 0.00632 / 0.36 ( 16) metal coordination : angle 1.06421 / 0.59 ( 12) *********************** 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 179 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.380 Fit side-chains REVERT: A 32 THR cc_start: 0.5787 (OUTLIER) cc_final: 0.5482 (p) REVERT: A 182 ASP cc_start: 0.7303 (t70) cc_final: 0.6907 (t70) REVERT: A 265 ILE cc_start: 0.8169 (mt) cc_final: 0.7734 (pt) REVERT: A 275 LYS cc_start: 0.7605 (mttt) cc_final: 0.6839 (tptp) REVERT: A 437 ASN cc_start: 0.8449 (t0) cc_final: 0.8094 (m110) REVERT: A 451 LYS cc_start: 0.7391 (mmpt) cc_final: 0.7138 (mttt) REVERT: B 32 THR cc_start: 0.5867 (OUTLIER) cc_final: 0.5556 (p) REVERT: B 182 ASP cc_start: 0.7278 (t70) cc_final: 0.6949 (t70) REVERT: B 265 ILE cc_start: 0.8198 (mt) cc_final: 0.7779 (pt) REVERT: B 275 LYS cc_start: 0.7598 (mttt) cc_final: 0.6857 (tptp) REVERT: B 437 ASN cc_start: 0.8445 (t0) cc_final: 0.8091 (m110) REVERT: B 451 LYS cc_start: 0.7360 (mmpt) cc_final: 0.7110 (mttt) REVERT: B 458 LYS cc_start: 0.7221 (mmmt) cc_final: 0.6941 (mtmt) REVERT: C 32 THR cc_start: 0.5883 (OUTLIER) cc_final: 0.5581 (p) REVERT: C 182 ASP cc_start: 0.7270 (t70) cc_final: 0.6865 (t70) REVERT: C 265 ILE cc_start: 0.8194 (mt) cc_final: 0.7783 (pt) REVERT: C 275 LYS cc_start: 0.7594 (mttt) cc_final: 0.6857 (tptp) REVERT: C 437 ASN cc_start: 0.8430 (t0) cc_final: 0.8084 (m110) REVERT: C 451 LYS cc_start: 0.7373 (mmpt) cc_final: 0.7119 (mttt) REVERT: D 32 THR cc_start: 0.5903 (OUTLIER) cc_final: 0.5602 (p) REVERT: D 182 ASP cc_start: 0.7307 (t70) cc_final: 0.6920 (t70) REVERT: D 265 ILE cc_start: 0.8176 (mt) cc_final: 0.7739 (pt) REVERT: D 275 LYS cc_start: 0.7584 (mttt) cc_final: 0.6843 (tptp) REVERT: D 437 ASN cc_start: 0.8449 (t0) cc_final: 0.8096 (m110) REVERT: D 451 LYS cc_start: 0.7384 (mmpt) cc_final: 0.7127 (mttt) outliers start: 21 outliers final: 15 residues processed: 174 average time/residue: 0.4351 time to fit residues: 83.9266 Evaluate side-chains 170 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.198245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139144 restraints weight = 14472.302| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.88 r_work: 0.2969 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2559 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= 0.136 Angle : 0.570 14.488 18084 Z= 0.274 Chirality : 0.040 0.134 1992 Planarity : 0.004 0.048 2244 Dihedral : 5.125 58.048 1772 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.56 % Allowed : 14.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.22), residues: 1552 helix: 1.22 (0.17), residues: 984 sheet: 2.70 (0.90), residues: 40 loop : -1.05 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 110 TYR 0.007 0.001 TYR A 365 PHE 0.018 0.001 PHE B 56 TRP 0.011 0.001 TRP B 392 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13276) covalent geometry : angle 0.56959 / 0.27 (18072) hydrogen bonds : bond 0.05811 / 3.93 ( 687) hydrogen bonds : angle 4.26028 / 3.02 ( 2010) metal coordination : bond 0.00573 / 0.32 ( 16) metal coordination : angle 1.02078 / 0.57 ( 12) ********************** 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: 21 poor density : 152 time to evaluate : 0.419 Fit side-chains REVERT: A 32 THR cc_start: 0.5958 (OUTLIER) cc_final: 0.5615 (p) REVERT: A 182 ASP cc_start: 0.7357 (t70) cc_final: 0.6954 (t70) REVERT: A 265 ILE cc_start: 0.8171 (mt) cc_final: 0.7724 (pt) REVERT: A 275 LYS cc_start: 0.7640 (mttt) cc_final: 0.6875 (tptp) REVERT: A 437 ASN cc_start: 0.8496 (t0) cc_final: 0.8172 (m110) REVERT: A 451 LYS cc_start: 0.7396 (mmpt) cc_final: 0.7143 (mttt) REVERT: B 32 THR cc_start: 0.5993 (OUTLIER) cc_final: 0.5680 (p) REVERT: B 182 ASP cc_start: 0.7343 (t70) cc_final: 0.7021 (t70) REVERT: B 265 ILE cc_start: 0.8195 (mt) cc_final: 0.7766 (pt) REVERT: B 275 LYS cc_start: 0.7638 (mttt) cc_final: 0.6880 (tptp) REVERT: B 437 ASN cc_start: 0.8489 (t0) cc_final: 0.8167 (m110) REVERT: B 451 LYS cc_start: 0.7356 (mmpt) cc_final: 0.7099 (mttt) REVERT: B 458 LYS cc_start: 0.7236 (mmmt) cc_final: 0.6980 (mtmt) REVERT: C 32 THR cc_start: 0.5930 (OUTLIER) cc_final: 0.5628 (p) REVERT: C 182 ASP cc_start: 0.7335 (t70) cc_final: 0.6938 (t70) REVERT: C 265 ILE cc_start: 0.8148 (mt) cc_final: 0.7734 (pt) REVERT: C 275 LYS cc_start: 0.7657 (mttt) cc_final: 0.6887 (tptp) REVERT: C 437 ASN cc_start: 0.8489 (t0) cc_final: 0.8170 (m110) REVERT: C 451 LYS cc_start: 0.7366 (mmpt) cc_final: 0.7128 (mttt) REVERT: D 32 THR cc_start: 0.5949 (OUTLIER) cc_final: 0.5647 (p) REVERT: D 182 ASP cc_start: 0.7368 (t70) cc_final: 0.6965 (t70) REVERT: D 265 ILE cc_start: 0.8170 (mt) cc_final: 0.7719 (pt) REVERT: D 275 LYS cc_start: 0.7637 (mttt) cc_final: 0.6874 (tptp) REVERT: D 437 ASN cc_start: 0.8496 (t0) cc_final: 0.8182 (m110) REVERT: D 451 LYS cc_start: 0.7389 (mmpt) cc_final: 0.7127 (mttt) outliers start: 21 outliers final: 15 residues processed: 168 average time/residue: 0.3939 time to fit residues: 74.2434 Evaluate side-chains 168 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 80 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 126 optimal weight: 0.3980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.197237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138264 restraints weight = 14415.666| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.91 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2621 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= 0.157 Angle : 0.596 14.426 18084 Z= 0.288 Chirality : 0.041 0.131 1992 Planarity : 0.004 0.049 2244 Dihedral : 5.158 59.283 1772 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.48 % Allowed : 15.21 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1552 helix: 1.15 (0.17), residues: 984 sheet: 2.66 (0.90), residues: 40 loop : -1.12 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 110 TYR 0.008 0.001 TYR B 365 PHE 0.018 0.001 PHE A 266 TRP 0.010 0.001 TRP D 392 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (13276) covalent geometry : angle 0.59585 / 0.29 (18072) hydrogen bonds : bond 0.06294 / 4.25 ( 687) hydrogen bonds : angle 4.31041 / 3.06 ( 2010) metal coordination : bond 0.00714 / 0.41 ( 16) metal coordination : angle 1.11810 / 0.63 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3774.72 seconds wall clock time: 64 minutes 56.92 seconds (3896.92 seconds total)