Starting phenix.real_space_refine on Fri Jul 3 06:52:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7phi_13417/07_2026/7phi_13417.cif Found real_map, /net/cci-nas-00/data/ceres_data/7phi_13417/07_2026/7phi_13417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7phi_13417/07_2026/7phi_13417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7phi_13417/07_2026/7phi_13417.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7phi_13417/07_2026/7phi_13417.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7phi_13417/07_2026/7phi_13417.cif" model { file = "/net/cci-nas-00/data/ceres_data/7phi_13417/07_2026/7phi_13417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7phi_13417/07_2026/7phi_13417.cif" } resolution = 3.1 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= 0.013 sd= 0.099 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 Zn 4 6.06 5 P 8 5.49 5 S 68 5.16 5 C 8328 2.51 5 N 2108 2.21 5 O 2188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 12708 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {' K': 4, ' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'PCF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "D" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 123 Unusual residues: {' ZN': 1, 'PCF': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 798 SG CYS A 104 66.417 45.251 46.373 1.00107.92 S ATOM 6825 SG CYS B 83 63.861 48.087 44.306 1.00103.76 S ATOM 3896 SG CYS C 104 49.470 68.990 46.280 1.00107.92 S ATOM 3902 SG CYS C 105 52.826 69.884 45.032 1.00105.62 S ATOM 9923 SG CYS D 83 52.151 66.104 44.334 1.00103.76 S ATOM 3727 SG CYS C 83 67.058 63.051 44.262 1.00103.76 S ATOM 6994 SG CYS B 104 69.820 65.671 46.295 1.00107.92 S ATOM 7000 SG CYS B 105 70.709 62.314 45.050 1.00105.62 S ATOM 629 SG CYS A 83 48.854 51.266 44.358 1.00103.76 S ATOM 10092 SG CYS D 104 46.102 48.552 46.344 1.00107.92 S ATOM 10098 SG CYS D 105 45.231 51.913 45.096 1.00105.62 S Time building chain proxies: 2.14, per 1000 atoms: 0.17 Number of scatterers: 12708 At special positions: 0 Unit cell: (115.92, 115.08, 124.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 K 4 19.00 S 68 16.00 P 8 15.00 O 2188 8.00 N 2108 7.00 C 8328 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: 0.99 Conformation dependent library (CDL) restraints added in 491.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 603 " - pdb=" SG CYS B 83 " pdb="ZN ZN A 603 " - 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 C 83 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 105 " pdb=" ZN C 602 " pdb="ZN ZN C 602 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 602 " - pdb=" SG CYS D 83 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 104 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 105 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 601 " - pdb=" SG CYS A 83 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 105 " Number of angles added : 9 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 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: 88 helices and 8 sheets defined 71.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 removed outlier: 4.532A pdb=" N LEU A 29 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.618A pdb=" N PHE A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N HIS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.555A pdb=" N ASP A 100 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.672A pdb=" N TYR A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.766A pdb=" N ARG A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 266 removed outlier: 3.692A pdb=" N THR A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 4.045A 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 Proline residue: A 288 - end of helix removed outlier: 3.792A pdb=" N GLU A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.766A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 320 through 326 removed outlier: 4.124A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.774A pdb=" N ARG A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 367 Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.738A pdb=" N GLY A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 431 through 452 Processing helix chain 'C' and resid 23 through 29 removed outlier: 4.532A pdb=" N LEU C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.618A pdb=" N PHE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.556A pdb=" N ASP C 100 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.951A 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 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.673A pdb=" N TYR C 109 " --> pdb=" O CYS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 182 through 185 Processing helix chain 'C' and resid 186 through 211 removed outlier: 3.766A pdb=" N ARG C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 266 removed outlier: 3.692A pdb=" N THR C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 4.044A 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 Proline residue: C 288 - end of helix removed outlier: 3.793A pdb=" N GLU C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.766A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 320 through 326 removed outlier: 4.123A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 341 removed outlier: 3.773A pdb=" N ARG C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 367 Processing helix chain 'C' and resid 386 through 399 removed outlier: 3.737A pdb=" N GLY C 390 " --> pdb=" O ASN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 431 through 452 Processing helix chain 'B' and resid 23 through 29 removed outlier: 4.532A pdb=" N LEU B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.619A pdb=" N PHE B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N HIS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.555A pdb=" N ASP B 100 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.951A 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 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 110 removed outlier: 3.672A pdb=" N TYR B 109 " --> pdb=" O CYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 186 through 211 removed outlier: 3.767A pdb=" N ARG B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 266 removed outlier: 3.693A pdb=" N THR B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 4.044A 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 Proline residue: B 288 - end of helix removed outlier: 3.793A pdb=" N GLU B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY B 294 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 315 removed outlier: 3.765A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 320 through 326 removed outlier: 4.123A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.774A pdb=" N ARG B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 367 Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.738A pdb=" N GLY B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 431 through 452 Processing helix chain 'D' and resid 23 through 29 removed outlier: 4.533A pdb=" N LEU D 29 " --> pdb=" O THR D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 60 through 74 removed outlier: 3.618A pdb=" N PHE D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.556A pdb=" N ASP D 100 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.951A 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 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.672A pdb=" N TYR D 109 " --> pdb=" O CYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 182 through 185 Processing helix chain 'D' and resid 186 through 211 removed outlier: 3.767A pdb=" N ARG D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 266 removed outlier: 3.692A pdb=" N THR D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 4.044A 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 Proline residue: D 288 - end of helix removed outlier: 3.793A pdb=" N GLU D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 removed outlier: 3.765A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 320 through 326 removed outlier: 4.123A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.773A pdb=" N ARG D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 367 Processing helix chain 'D' and resid 386 through 399 removed outlier: 3.738A pdb=" N GLY D 390 " --> pdb=" O ASN D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 431 through 452 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.850A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 49 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.692A pdb=" N GLU A 238 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 22 removed outlier: 3.851A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP C 49 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 218 through 221 removed outlier: 3.692A pdb=" N GLU C 238 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.850A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 49 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 218 through 221 removed outlier: 3.692A pdb=" N GLU B 238 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 17 through 22 removed outlier: 3.849A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP D 49 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 218 through 221 removed outlier: 3.692A pdb=" N GLU D 238 " --> pdb=" O VAL D 219 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2208 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: 1.83 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1932 1.31 - 1.43: 3790 1.43 - 1.56: 7214 1.56 - 1.68: 20 1.68 - 1.81: 104 Bond restraints: 13060 Sorted by residual: bond pdb=" C21 PCF C 601 " pdb=" O21 PCF C 601 " ideal model delta sigma weight residual 1.334 1.436 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C21 PCF D 604 " pdb=" O21 PCF D 604 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C21 PCF A 602 " pdb=" O21 PCF A 602 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C21 PCF B 603 " pdb=" O21 PCF B 603 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C21 PCF A 601 " pdb=" O21 PCF A 601 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 13055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 17436 3.11 - 6.21: 280 6.21 - 9.32: 44 9.32 - 12.42: 0 12.42 - 15.53: 8 Bond angle restraints: 17768 Sorted by residual: angle pdb=" O12 PCF B 603 " pdb=" P PCF B 603 " pdb=" O14 PCF B 603 " ideal model delta sigma weight residual 123.69 108.16 15.53 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O12 PCF A 602 " pdb=" P PCF A 602 " pdb=" O14 PCF A 602 " ideal model delta sigma weight residual 123.69 108.17 15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O12 PCF D 604 " pdb=" P PCF D 604 " pdb=" O14 PCF D 604 " ideal model delta sigma weight residual 123.69 108.19 15.50 3.00e+00 1.11e-01 2.67e+01 angle pdb=" O12 PCF C 601 " pdb=" P PCF C 601 " pdb=" O14 PCF C 601 " ideal model delta sigma weight residual 123.69 108.20 15.49 3.00e+00 1.11e-01 2.67e+01 angle pdb=" O12 PCF A 601 " pdb=" P PCF A 601 " pdb=" O14 PCF A 601 " ideal model delta sigma weight residual 123.69 108.80 14.89 3.00e+00 1.11e-01 2.46e+01 ... (remaining 17763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.73: 7371 28.73 - 57.46: 301 57.46 - 86.18: 40 86.18 - 114.91: 4 114.91 - 143.64: 4 Dihedral angle restraints: 7720 sinusoidal: 3132 harmonic: 4588 Sorted by residual: dihedral pdb=" O21 PCF B 602 " pdb=" C2 PCF B 602 " pdb=" C3 PCF B 602 " pdb=" O31 PCF B 602 " ideal model delta sinusoidal sigma weight residual 59.47 -84.17 143.64 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" O21 PCF D 603 " pdb=" C2 PCF D 603 " pdb=" C3 PCF D 603 " pdb=" O31 PCF D 603 " ideal model delta sinusoidal sigma weight residual 59.47 -84.16 143.63 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" O21 PCF D 602 " pdb=" C2 PCF D 602 " pdb=" C3 PCF D 602 " pdb=" O31 PCF D 602 " ideal model delta sinusoidal sigma weight residual 59.47 -84.15 143.62 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 7717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1254 0.046 - 0.092: 576 0.092 - 0.138: 86 0.138 - 0.185: 32 0.185 - 0.231: 4 Chirality restraints: 1952 Sorted by residual: chirality pdb=" C2 PCF D 604 " pdb=" C1 PCF D 604 " pdb=" C3 PCF D 604 " pdb=" O21 PCF D 604 " both_signs ideal model delta sigma weight residual False -2.60 -2.36 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C2 PCF A 602 " pdb=" C1 PCF A 602 " pdb=" C3 PCF A 602 " pdb=" O21 PCF A 602 " both_signs ideal model delta sigma weight residual False -2.60 -2.37 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C2 PCF C 601 " pdb=" C1 PCF C 601 " pdb=" C3 PCF C 601 " pdb=" O21 PCF C 601 " both_signs ideal model delta sigma weight residual False -2.60 -2.37 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1949 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 190 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ARG A 190 " 0.055 2.00e-02 2.50e+03 pdb=" O ARG A 190 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR A 191 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 190 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ARG D 190 " 0.055 2.00e-02 2.50e+03 pdb=" O ARG D 190 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR D 191 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 190 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ARG C 190 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG C 190 " 0.021 2.00e-02 2.50e+03 pdb=" N TYR C 191 " 0.019 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 4114 2.84 - 3.41: 14253 3.41 - 3.99: 22539 3.99 - 4.56: 32923 4.56 - 5.14: 47384 Nonbonded interactions: 121213 Sorted by model distance: nonbonded pdb=" NH1 ARG D 113 " pdb=" OE1 GLU D 116 " model vdw 2.265 3.120 nonbonded pdb=" NH1 ARG A 113 " pdb=" OE1 GLU A 116 " model vdw 2.265 3.120 nonbonded pdb=" NH1 ARG C 113 " pdb=" OE1 GLU C 116 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG B 113 " pdb=" OE1 GLU B 116 " model vdw 2.266 3.120 nonbonded pdb=" OG1 THR A 32 " pdb=" OH TYR A 71 " model vdw 2.282 3.040 ... (remaining 121208 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 464) selection = (chain 'B' and resid 7 through 464) selection = (chain 'C' and resid 7 through 464) selection = (chain 'D' and resid 7 through 464) } 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: 1.670 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.940 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 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 : 0.014 0.626 13075 Z= 0.551 Angle : 1.094 28.742 17777 Z= 0.471 Chirality : 0.052 0.231 1952 Planarity : 0.006 0.054 2220 Dihedral : 15.599 143.640 4744 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % 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: -1.29 (0.19), residues: 1540 helix: -0.49 (0.15), residues: 960 sheet: 0.42 (0.69), residues: 40 loop : -1.43 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 18 TYR 0.020 0.003 TYR C 70 PHE 0.025 0.002 PHE B 207 TRP 0.013 0.002 TRP B 172 HIS 0.009 0.002 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00993 / 0.43 (13060) covalent geometry : angle 0.96264 / 0.45 (17768) hydrogen bonds : bond 0.12092 / 7.96 ( 752) hydrogen bonds : angle 6.33042 / 4.70 ( 2208) metal coordination : bond 0.28021 / 19.21 ( 15) metal coordination : angle 23.13489 / 12.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.353 Fit side-chains REVERT: A 54 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6467 (pt0) REVERT: A 116 GLU cc_start: 0.6569 (tt0) cc_final: 0.6333 (tt0) REVERT: A 339 ARG cc_start: 0.6898 (ttt180) cc_final: 0.6175 (mtt90) REVERT: A 458 LYS cc_start: 0.7267 (mmtp) cc_final: 0.6888 (tptp) REVERT: C 116 GLU cc_start: 0.6519 (tt0) cc_final: 0.6272 (tt0) REVERT: C 339 ARG cc_start: 0.6927 (ttt180) cc_final: 0.6162 (mtt90) REVERT: C 380 GLU cc_start: 0.6500 (tp30) cc_final: 0.6267 (mm-30) REVERT: B 54 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6130 (pt0) REVERT: B 116 GLU cc_start: 0.6415 (tt0) cc_final: 0.6209 (tt0) REVERT: B 339 ARG cc_start: 0.7277 (ttt180) cc_final: 0.6620 (mtt90) REVERT: D 54 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6422 (pt0) REVERT: D 89 GLU cc_start: 0.6422 (tm-30) cc_final: 0.6014 (tm-30) REVERT: D 339 ARG cc_start: 0.7021 (ttt180) cc_final: 0.6323 (mtt90) REVERT: D 380 GLU cc_start: 0.6465 (tp30) cc_final: 0.6166 (mm-30) REVERT: D 430 MET cc_start: 0.7126 (mmt) cc_final: 0.6887 (mmt) REVERT: D 458 LYS cc_start: 0.7387 (mmtp) cc_final: 0.6685 (tptp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1182 time to fit residues: 31.5443 Evaluate side-chains 144 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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: 0.3980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN A 111 GLN A 450 GLN C 20 GLN C 111 GLN C 279 ASN B 20 GLN B 111 GLN B 279 ASN B 450 GLN D 20 GLN D 111 GLN D 279 ASN D 450 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.221513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.197059 restraints weight = 12813.444| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.14 r_work: 0.3832 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13075 Z= 0.139 Angle : 0.515 6.163 17777 Z= 0.264 Chirality : 0.040 0.151 1952 Planarity : 0.005 0.042 2220 Dihedral : 12.742 137.510 2036 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.66 % Allowed : 8.94 % Favored : 89.40 % 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 (0.21), residues: 1540 helix: 1.06 (0.16), residues: 948 sheet: -0.50 (0.74), residues: 56 loop : -0.02 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.011 0.001 TYR B 71 PHE 0.010 0.001 PHE D 207 TRP 0.014 0.001 TRP A 177 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (13060) covalent geometry : angle 0.51175 / 0.26 (17768) hydrogen bonds : bond 0.05555 / 3.61 ( 752) hydrogen bonds : angle 4.72160 / 3.47 ( 2208) metal coordination : bond 0.01031 / 0.53 ( 15) metal coordination : angle 2.62059 / 1.28 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 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: 21 poor density : 173 time to evaluate : 0.322 Fit side-chains REVERT: D 89 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7622 (tm-30) outliers start: 21 outliers final: 12 residues processed: 186 average time/residue: 0.1279 time to fit residues: 32.2887 Evaluate side-chains 147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 GLN C 112 HIS C 279 ASN C 450 GLN B 112 HIS B 450 GLN D 279 ASN D 450 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.217524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.191636 restraints weight = 12950.319| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 1.12 r_work: 0.3757 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13075 Z= 0.185 Angle : 0.540 7.257 17777 Z= 0.276 Chirality : 0.042 0.143 1952 Planarity : 0.005 0.043 2220 Dihedral : 12.398 138.394 2036 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.66 % Allowed : 9.89 % Favored : 88.45 % 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: 0.92 (0.21), residues: 1540 helix: 1.07 (0.16), residues: 992 sheet: -0.10 (0.51), residues: 96 loop : -0.03 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.012 0.001 TYR C 70 PHE 0.017 0.001 PHE D 207 TRP 0.007 0.001 TRP A 392 HIS 0.004 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (13060) covalent geometry : angle 0.53712 / 0.28 (17768) hydrogen bonds : bond 0.06002 / 3.92 ( 752) hydrogen bonds : angle 4.57219 / 3.32 ( 2208) metal coordination : bond 0.00747 / 0.39 ( 15) metal coordination : angle 2.46117 / 1.36 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.407 Fit side-chains REVERT: D 89 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7604 (tm-30) REVERT: D 451 LYS cc_start: 0.6752 (ttmm) cc_final: 0.6290 (tttt) outliers start: 21 outliers final: 15 residues processed: 146 average time/residue: 0.1075 time to fit residues: 21.9960 Evaluate side-chains 136 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 52 optimal weight: 2.9990 chunk 116 optimal weight: 0.1980 chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 127 optimal weight: 0.0770 chunk 65 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.221917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.197388 restraints weight = 12909.077| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.11 r_work: 0.3749 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13075 Z= 0.115 Angle : 0.471 6.006 17777 Z= 0.238 Chirality : 0.039 0.151 1952 Planarity : 0.004 0.040 2220 Dihedral : 12.174 134.709 2036 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.06 % Allowed : 11.16 % Favored : 86.79 % 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: 1.57 (0.21), residues: 1540 helix: 1.53 (0.17), residues: 968 sheet: -0.20 (0.76), residues: 56 loop : 0.43 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.007 0.001 TYR B 70 PHE 0.015 0.001 PHE C 93 TRP 0.006 0.001 TRP A 392 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (13060) covalent geometry : angle 0.47013 / 0.24 (17768) hydrogen bonds : bond 0.04888 / 3.19 ( 752) hydrogen bonds : angle 4.19748 / 3.05 ( 2208) metal coordination : bond 0.00338 / 0.18 ( 15) metal coordination : angle 1.55753 / 0.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.411 Fit side-chains REVERT: C 216 ASN cc_start: 0.8503 (m-40) cc_final: 0.8292 (m-40) REVERT: C 262 MET cc_start: 0.6700 (ppp) cc_final: 0.6417 (ppp) REVERT: D 89 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7839 (tm-30) REVERT: D 451 LYS cc_start: 0.6976 (ttmm) cc_final: 0.6415 (tttt) REVERT: D 458 LYS cc_start: 0.7742 (tptp) cc_final: 0.7412 (tptt) outliers start: 26 outliers final: 16 residues processed: 160 average time/residue: 0.1216 time to fit residues: 27.6323 Evaluate side-chains 139 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 GLN C 43 HIS C 279 ASN B 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.218703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.193530 restraints weight = 13017.165| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.09 r_work: 0.3739 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13075 Z= 0.147 Angle : 0.495 6.461 17777 Z= 0.252 Chirality : 0.041 0.200 1952 Planarity : 0.005 0.042 2220 Dihedral : 12.035 134.552 2036 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.98 % Allowed : 12.26 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.64 (0.21), residues: 1540 helix: 1.52 (0.17), residues: 972 sheet: 0.18 (0.51), residues: 96 loop : 0.59 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 320 TYR 0.014 0.001 TYR C 70 PHE 0.015 0.001 PHE C 93 TRP 0.006 0.001 TRP A 392 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (13060) covalent geometry : angle 0.49314 / 0.25 (17768) hydrogen bonds : bond 0.05346 / 3.48 ( 752) hydrogen bonds : angle 4.25655 / 3.08 ( 2208) metal coordination : bond 0.00567 / 0.29 ( 15) metal coordination : angle 1.71557 / 0.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.457 Fit side-chains REVERT: C 43 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.6744 (m90) outliers start: 25 outliers final: 15 residues processed: 148 average time/residue: 0.1230 time to fit residues: 25.7991 Evaluate side-chains 141 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 HIS A 112 HIS A 450 GLN C 22 HIS B 22 HIS B 43 HIS D 22 HIS D 43 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.215696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.189732 restraints weight = 12906.146| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 1.09 r_work: 0.3756 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13075 Z= 0.208 Angle : 0.551 7.511 17777 Z= 0.282 Chirality : 0.043 0.218 1952 Planarity : 0.005 0.045 2220 Dihedral : 12.113 137.536 2036 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.98 % Allowed : 13.37 % Favored : 84.65 % 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: 1.43 (0.21), residues: 1540 helix: 1.34 (0.17), residues: 972 sheet: 0.14 (0.51), residues: 96 loop : 0.52 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.013 0.001 TYR A 70 PHE 0.017 0.002 PHE A 93 TRP 0.008 0.001 TRP A 392 HIS 0.015 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (13060) covalent geometry : angle 0.54896 / 0.28 (17768) hydrogen bonds : bond 0.06132 / 3.99 ( 752) hydrogen bonds : angle 4.47293 / 3.24 ( 2208) metal coordination : bond 0.01044 / 0.52 ( 15) metal coordination : angle 2.22053 / 1.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.450 Fit side-chains REVERT: B 43 HIS cc_start: 0.7130 (OUTLIER) cc_final: 0.6533 (m90) REVERT: B 262 MET cc_start: 0.6857 (ppp) cc_final: 0.6575 (ppp) REVERT: D 43 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.6423 (m90) outliers start: 25 outliers final: 20 residues processed: 148 average time/residue: 0.1227 time to fit residues: 25.8124 Evaluate side-chains 146 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 51 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 450 GLN C 43 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.217714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.192218 restraints weight = 12940.813| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.09 r_work: 0.3677 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13075 Z= 0.155 Angle : 0.509 6.760 17777 Z= 0.259 Chirality : 0.041 0.195 1952 Planarity : 0.005 0.044 2220 Dihedral : 11.969 135.800 2036 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.98 % Allowed : 14.56 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1540 helix: 1.45 (0.17), residues: 972 sheet: 0.21 (0.78), residues: 56 loop : 0.45 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.010 0.001 TYR C 70 PHE 0.018 0.001 PHE D 93 TRP 0.007 0.001 TRP A 392 HIS 0.007 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (13060) covalent geometry : angle 0.50768 / 0.26 (17768) hydrogen bonds : bond 0.05448 / 3.54 ( 752) hydrogen bonds : angle 4.33981 / 3.14 ( 2208) metal coordination : bond 0.00697 / 0.35 ( 15) metal coordination : angle 1.88689 / 1.02 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.312 Fit side-chains REVERT: A 43 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.6723 (m90) REVERT: B 262 MET cc_start: 0.6527 (ppp) cc_final: 0.6147 (ppp) outliers start: 25 outliers final: 18 residues processed: 147 average time/residue: 0.1251 time to fit residues: 25.6926 Evaluate side-chains 145 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS C 43 HIS B 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 = 0.4355 r_free = 0.4355 target = 0.219348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.194306 restraints weight = 12758.025| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.11 r_work: 0.3698 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13075 Z= 0.128 Angle : 0.486 6.527 17777 Z= 0.245 Chirality : 0.040 0.198 1952 Planarity : 0.004 0.043 2220 Dihedral : 11.758 133.552 2036 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.82 % Allowed : 15.11 % Favored : 83.07 % 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: 1.72 (0.22), residues: 1540 helix: 1.60 (0.17), residues: 972 sheet: 0.22 (0.77), residues: 56 loop : 0.53 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.016 0.001 TYR B 70 PHE 0.017 0.001 PHE D 93 TRP 0.007 0.001 TRP A 392 HIS 0.017 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (13060) covalent geometry : angle 0.48498 / 0.25 (17768) hydrogen bonds : bond 0.05032 / 3.27 ( 752) hydrogen bonds : angle 4.22174 / 3.06 ( 2208) metal coordination : bond 0.00489 / 0.24 ( 15) metal coordination : angle 1.66681 / 0.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.277 Fit side-chains REVERT: A 43 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.6742 (m90) REVERT: C 43 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.6772 (m90) REVERT: B 262 MET cc_start: 0.6555 (ppp) cc_final: 0.6294 (ppp) REVERT: B 458 LYS cc_start: 0.7309 (ttmt) cc_final: 0.6849 (tptp) REVERT: D 43 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.6749 (m90) outliers start: 23 outliers final: 18 residues processed: 147 average time/residue: 0.1074 time to fit residues: 22.1390 Evaluate side-chains 147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 66 HIS C 43 HIS D 43 HIS D 66 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.219945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.195339 restraints weight = 12956.492| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.12 r_work: 0.3709 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13075 Z= 0.122 Angle : 0.480 6.566 17777 Z= 0.241 Chirality : 0.040 0.198 1952 Planarity : 0.004 0.043 2220 Dihedral : 11.619 132.309 2036 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.06 % Allowed : 14.79 % Favored : 83.15 % 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: 1.82 (0.22), residues: 1540 helix: 1.67 (0.17), residues: 972 sheet: 0.16 (0.75), residues: 56 loop : 0.60 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.016 0.001 TYR C 70 PHE 0.016 0.001 PHE D 93 TRP 0.007 0.001 TRP A 392 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13060) covalent geometry : angle 0.47846 / 0.24 (17768) hydrogen bonds : bond 0.04899 / 3.18 ( 752) hydrogen bonds : angle 4.16862 / 3.02 ( 2208) metal coordination : bond 0.00428 / 0.21 ( 15) metal coordination : angle 1.55304 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.324 Fit side-chains REVERT: A 43 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.7052 (m90) REVERT: B 8 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: B 262 MET cc_start: 0.6510 (ppp) cc_final: 0.6233 (ppp) REVERT: B 458 LYS cc_start: 0.7325 (ttmt) cc_final: 0.6827 (tptp) outliers start: 26 outliers final: 20 residues processed: 148 average time/residue: 0.1219 time to fit residues: 25.5032 Evaluate side-chains 148 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 100 optimal weight: 0.0470 chunk 34 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 450 GLN C 43 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.217650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.194949 restraints weight = 12987.364| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 1.06 r_work: 0.3705 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13075 Z= 0.161 Angle : 0.510 6.881 17777 Z= 0.259 Chirality : 0.042 0.212 1952 Planarity : 0.005 0.043 2220 Dihedral : 11.548 133.152 2036 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.98 % Allowed : 14.87 % Favored : 83.15 % 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: 1.71 (0.22), residues: 1540 helix: 1.58 (0.17), residues: 972 sheet: 0.05 (0.49), residues: 96 loop : 0.63 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.018 0.001 TYR C 70 PHE 0.015 0.001 PHE B 93 TRP 0.007 0.001 TRP A 392 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (13060) covalent geometry : angle 0.50900 / 0.26 (17768) hydrogen bonds : bond 0.05411 / 3.52 ( 752) hydrogen bonds : angle 4.27899 / 3.10 ( 2208) metal coordination : bond 0.00698 / 0.35 ( 15) metal coordination : angle 1.75210 / 0.96 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.268 Fit side-chains REVERT: A 43 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.7059 (m90) REVERT: C 43 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6560 (m90) REVERT: B 8 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7244 (tp30) REVERT: B 262 MET cc_start: 0.6550 (ppp) cc_final: 0.6313 (ppp) REVERT: B 458 LYS cc_start: 0.7305 (ttmt) cc_final: 0.6856 (tptp) outliers start: 25 outliers final: 21 residues processed: 141 average time/residue: 0.1070 time to fit residues: 21.2410 Evaluate side-chains 148 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 126 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 0.0170 chunk 121 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.216448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.193179 restraints weight = 12992.993| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.07 r_work: 0.3683 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13075 Z= 0.190 Angle : 0.536 7.110 17777 Z= 0.273 Chirality : 0.043 0.214 1952 Planarity : 0.005 0.044 2220 Dihedral : 11.566 134.435 2036 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.82 % Allowed : 14.79 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.58 (0.21), residues: 1540 helix: 1.50 (0.17), residues: 972 sheet: -0.05 (0.49), residues: 96 loop : 0.55 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.017 0.001 TYR C 70 PHE 0.015 0.001 PHE B 93 TRP 0.008 0.001 TRP A 392 HIS 0.010 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (13060) covalent geometry : angle 0.53435 / 0.27 (17768) hydrogen bonds : bond 0.05738 / 3.73 ( 752) hydrogen bonds : angle 4.38154 / 3.17 ( 2208) metal coordination : bond 0.00892 / 0.45 ( 15) metal coordination : angle 1.93744 / 1.08 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3113.59 seconds wall clock time: 53 minutes 48.56 seconds (3228.56 seconds total)