Starting phenix.real_space_refine on Fri Jul 3 21:16:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ekp_31172/07_2026/7ekp_31172.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekp_31172/07_2026/7ekp_31172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ekp_31172/07_2026/7ekp_31172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekp_31172/07_2026/7ekp_31172.map" model { file = "/net/cci-nas-00/data/ceres_data/7ekp_31172/07_2026/7ekp_31172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekp_31172/07_2026/7ekp_31172.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ekp_31172/07_2026/7ekp_31172.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ekp_31172/07_2026/7ekp_31172.cif" } resolution = 2.85 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= 0.011 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 120 5.16 5 Cl 5 4.86 5 C 10575 2.51 5 N 2570 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 16115 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3132 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 3201 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'CLR': 1, 'I33': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 3.40, per 1000 atoms: 0.21 Number of scatterers: 16115 At special positions: 0 Unit cell: (92.274, 91.26, 163.254, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 5 17.00 S 120 16.00 O 2845 8.00 N 2570 7.00 C 10575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 602 " - " ASN A 46 " " NAG B 602 " - " ASN B 46 " " NAG C 602 " - " ASN C 46 " " NAG D 602 " - " ASN D 46 " " NAG E 602 " - " ASN E 46 " " NAG F 1 " - " ASN A 133 " " NAG G 1 " - " ASN B 133 " " NAG H 1 " - " ASN C 133 " " NAG I 1 " - " ASN D 133 " " NAG J 1 " - " ASN E 133 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 44.2% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.563A pdb=" N LYS A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 237 through 249 removed outlier: 3.572A pdb=" N CYS A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.511A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 removed outlier: 4.035A pdb=" N LEU A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 319 removed outlier: 3.551A pdb=" N VAL A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 433 through 490 removed outlier: 3.753A pdb=" N ALA A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.618A pdb=" N ALA A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.564A pdb=" N LYS B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 237 through 249 removed outlier: 3.572A pdb=" N CYS B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 260 through 273 removed outlier: 3.511A pdb=" N VAL B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 removed outlier: 4.034A pdb=" N LEU B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 278 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 319 removed outlier: 3.551A pdb=" N VAL B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 433 through 490 removed outlier: 3.754A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.618A pdb=" N ALA B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.563A pdb=" N LYS C 31 " --> pdb=" O ARG C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 159 Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 237 through 249 removed outlier: 3.572A pdb=" N CYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.511A pdb=" N VAL C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 283 removed outlier: 4.034A pdb=" N LEU C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 278 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 319 removed outlier: 3.551A pdb=" N VAL C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 433 through 490 removed outlier: 3.753A pdb=" N ALA C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 501 removed outlier: 3.618A pdb=" N ALA C 496 " --> pdb=" O ASN C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.563A pdb=" N LYS D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 159 Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 237 through 249 removed outlier: 3.572A pdb=" N CYS D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 260 through 273 removed outlier: 3.510A pdb=" N VAL D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 283 removed outlier: 4.035A pdb=" N LEU D 277 " --> pdb=" O THR D 273 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 278 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 319 removed outlier: 3.551A pdb=" N VAL D 308 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 433 through 490 removed outlier: 3.754A pdb=" N ALA D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 removed outlier: 3.618A pdb=" N ALA D 496 " --> pdb=" O ASN D 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.563A pdb=" N LYS E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 159 Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 237 through 249 removed outlier: 3.572A pdb=" N CYS E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 260 through 273 removed outlier: 3.511A pdb=" N VAL E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 283 removed outlier: 4.034A pdb=" N LEU E 277 " --> pdb=" O THR E 273 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 278 " --> pdb=" O VAL E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 319 removed outlier: 3.551A pdb=" N VAL E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 433 through 490 removed outlier: 3.753A pdb=" N ALA E 490 " --> pdb=" O ILE E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 501 removed outlier: 3.618A pdb=" N ALA E 496 " --> pdb=" O ASN E 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 7.059A pdb=" N VAL A 71 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP A 64 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR A 73 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE A 62 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN A 75 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A 79 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR A 83 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 52 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU A 51 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN A 181 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 53 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.485A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.485A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 7.059A pdb=" N VAL B 71 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP B 64 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR B 73 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN B 75 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 79 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 83 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR B 52 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.485A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.485A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 removed outlier: 7.059A pdb=" N VAL C 71 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP C 64 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN C 75 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN C 79 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR C 83 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR C 52 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU C 51 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN C 181 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 53 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.485A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.485A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 102 removed outlier: 7.060A pdb=" N VAL D 71 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP D 64 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN D 75 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 79 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR D 83 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR D 52 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU D 51 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN D 181 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL D 53 " --> pdb=" O GLN D 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.485A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.485A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 102 removed outlier: 7.059A pdb=" N VAL E 71 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP E 64 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN E 75 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN E 79 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR E 83 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR E 52 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.486A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.486A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) 906 hydrogen bonds defined for protein. 2613 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: 2.78 Time building geometry restraints manager: 1.86 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: 2465 1.31 - 1.44: 4695 1.44 - 1.57: 9175 1.57 - 1.70: 60 1.70 - 1.83: 185 Bond restraints: 16580 Sorted by residual: bond pdb=" C02 I33 D 601 " pdb=" N13 I33 D 601 " ideal model delta sigma weight residual 1.339 1.450 -0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C02 I33 C 601 " pdb=" N13 I33 C 601 " ideal model delta sigma weight residual 1.339 1.450 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C02 I33 A 601 " pdb=" N13 I33 A 601 " ideal model delta sigma weight residual 1.339 1.450 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C02 I33 E 601 " pdb=" N13 I33 E 601 " ideal model delta sigma weight residual 1.339 1.449 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C02 I33 B 601 " pdb=" N13 I33 B 601 " ideal model delta sigma weight residual 1.339 1.449 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 16575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 22363 2.63 - 5.26: 232 5.26 - 7.89: 55 7.89 - 10.52: 10 10.52 - 13.14: 10 Bond angle restraints: 22670 Sorted by residual: angle pdb=" C02 I33 B 601 " pdb=" C03 I33 B 601 " pdb=" S12 I33 B 601 " ideal model delta sigma weight residual 115.03 128.17 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" C02 I33 C 601 " pdb=" C03 I33 C 601 " pdb=" S12 I33 C 601 " ideal model delta sigma weight residual 115.03 128.16 -13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" C02 I33 D 601 " pdb=" C03 I33 D 601 " pdb=" S12 I33 D 601 " ideal model delta sigma weight residual 115.03 128.16 -13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" C02 I33 E 601 " pdb=" C03 I33 E 601 " pdb=" S12 I33 E 601 " ideal model delta sigma weight residual 115.03 128.16 -13.13 3.00e+00 1.11e-01 1.91e+01 angle pdb=" C02 I33 A 601 " pdb=" C03 I33 A 601 " pdb=" S12 I33 A 601 " ideal model delta sigma weight residual 115.03 128.15 -13.12 3.00e+00 1.11e-01 1.91e+01 ... (remaining 22665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 8745 17.65 - 35.31: 625 35.31 - 52.96: 145 52.96 - 70.62: 30 70.62 - 88.27: 5 Dihedral angle restraints: 9550 sinusoidal: 3705 harmonic: 5845 Sorted by residual: dihedral pdb=" CA CYS D 212 " pdb=" C CYS D 212 " pdb=" N CYS D 213 " pdb=" CA CYS D 213 " ideal model delta harmonic sigma weight residual 180.00 -154.92 -25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA CYS A 212 " pdb=" C CYS A 212 " pdb=" N CYS A 213 " pdb=" CA CYS A 213 " ideal model delta harmonic sigma weight residual 180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA CYS B 212 " pdb=" C CYS B 212 " pdb=" N CYS B 213 " pdb=" CA CYS B 213 " ideal model delta harmonic sigma weight residual -180.00 -154.95 -25.05 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 9547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2585 0.127 - 0.255: 15 0.255 - 0.382: 10 0.382 - 0.510: 5 0.510 - 0.637: 20 Chirality restraints: 2635 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 133 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 1.01e+01 ... (remaining 2632 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 260 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CD GLU E 260 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU E 260 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU E 260 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 260 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" CD GLU D 260 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU D 260 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU D 260 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 260 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" CD GLU A 260 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 260 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 260 " -0.010 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4090 2.80 - 3.33: 14548 3.33 - 3.85: 25752 3.85 - 4.38: 29944 4.38 - 4.90: 53151 Nonbonded interactions: 127485 Sorted by model distance: nonbonded pdb=" O SER D 263 " pdb=" OG1 THR D 267 " model vdw 2.280 3.040 nonbonded pdb=" O SER E 263 " pdb=" OG1 THR E 267 " model vdw 2.280 3.040 nonbonded pdb=" O SER C 263 " pdb=" OG1 THR C 267 " model vdw 2.281 3.040 nonbonded pdb=" O SER A 263 " pdb=" OG1 THR A 267 " model vdw 2.281 3.040 nonbonded pdb=" O SER B 263 " pdb=" OG1 THR B 267 " model vdw 2.281 3.040 ... (remaining 127480 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.020 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.007 0.111 16605 Z= 0.339 Angle : 0.793 13.144 22735 Z= 0.339 Chirality : 0.070 0.637 2635 Planarity : 0.003 0.023 2760 Dihedral : 13.137 88.272 5740 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.88 % Allowed : 2.41 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.18), residues: 1965 helix: 0.54 (0.18), residues: 770 sheet: -0.31 (0.24), residues: 465 loop : -2.01 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 332 TYR 0.007 0.001 TYR B 140 PHE 0.009 0.001 PHE A 275 TRP 0.017 0.001 TRP D 176 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.34 (16580) covalent geometry : angle 0.75153 / 0.33 (22670) SS BOND : bond 0.00756 / 0.49 ( 10) SS BOND : angle 1.21014 / 0.89 ( 20) hydrogen bonds : bond 0.27372 / 17.68 ( 806) hydrogen bonds : angle 8.07975 / 5.68 ( 2613) link_BETA1-4 : bond 0.00145 / 0.09 ( 5) link_BETA1-4 : angle 4.13590 / 2.42 ( 15) link_NAG-ASN : bond 0.00347 / 0.22 ( 10) link_NAG-ASN : angle 6.36943 / 4.19 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 239 time to evaluate : 0.664 Fit side-chains REVERT: A 66 ASP cc_start: 0.8126 (t0) cc_final: 0.7836 (t0) REVERT: B 66 ASP cc_start: 0.7823 (t0) cc_final: 0.7506 (t70) REVERT: B 453 SER cc_start: 0.7014 (t) cc_final: 0.6798 (t) REVERT: C 63 MET cc_start: 0.8976 (mmm) cc_final: 0.8521 (mmm) REVERT: C 453 SER cc_start: 0.6941 (t) cc_final: 0.6728 (t) REVERT: D 66 ASP cc_start: 0.7860 (t0) cc_final: 0.7548 (t0) REVERT: D 151 TYR cc_start: 0.8310 (t80) cc_final: 0.7938 (t80) REVERT: E 176 TRP cc_start: 0.7467 (m-90) cc_final: 0.7258 (m100) REVERT: E 469 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7670 (tpp80) REVERT: E 473 MET cc_start: 0.6616 (mmt) cc_final: 0.6395 (mmm) outliers start: 15 outliers final: 0 residues processed: 239 average time/residue: 0.5184 time to fit residues: 138.8191 Evaluate side-chains 169 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.0770 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN A 69 ASN A 193 ASN A 236 ASN B 61 GLN B 193 ASN B 236 ASN C 193 ASN C 236 ASN D 61 GLN D 193 ASN D 236 ASN E 193 ASN E 236 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.097152 restraints weight = 44477.010| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.49 r_work: 0.2980 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16605 Z= 0.150 Angle : 0.681 12.257 22735 Z= 0.332 Chirality : 0.046 0.434 2635 Planarity : 0.004 0.029 2760 Dihedral : 4.651 29.633 2215 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.00 % Allowed : 7.35 % Favored : 91.65 % 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: -0.54 (0.18), residues: 1965 helix: 0.96 (0.18), residues: 780 sheet: 0.22 (0.25), residues: 440 loop : -2.21 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 332 TYR 0.014 0.001 TYR D 442 PHE 0.009 0.001 PHE B 493 TRP 0.014 0.001 TRP A 176 HIS 0.002 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (16580) covalent geometry : angle 0.64532 / 0.32 (22670) SS BOND : bond 0.00739 / 0.48 ( 10) SS BOND : angle 1.25017 / 0.93 ( 20) hydrogen bonds : bond 0.07613 / 4.92 ( 806) hydrogen bonds : angle 5.17412 / 3.64 ( 2613) link_BETA1-4 : bond 0.00222 / 0.15 ( 5) link_BETA1-4 : angle 1.64663 / 0.98 ( 15) link_NAG-ASN : bond 0.00773 / 0.50 ( 10) link_NAG-ASN : angle 5.82296 / 3.83 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.596 Fit side-chains REVERT: A 66 ASP cc_start: 0.7782 (t0) cc_final: 0.7327 (t0) REVERT: B 66 ASP cc_start: 0.7715 (t0) cc_final: 0.7403 (t70) REVERT: C 63 MET cc_start: 0.8716 (mmm) cc_final: 0.8160 (mmm) REVERT: C 257 ASP cc_start: 0.7407 (m-30) cc_final: 0.6943 (t0) REVERT: D 66 ASP cc_start: 0.7727 (t0) cc_final: 0.7320 (t0) REVERT: D 151 TYR cc_start: 0.8245 (t80) cc_final: 0.7815 (t80) REVERT: D 345 MET cc_start: 0.7470 (mmt) cc_final: 0.7076 (mmt) REVERT: E 176 TRP cc_start: 0.7739 (m-90) cc_final: 0.7532 (m-90) outliers start: 17 outliers final: 3 residues processed: 209 average time/residue: 0.4013 time to fit residues: 97.0079 Evaluate side-chains 172 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain D residue 47 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 158 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 193 ASN E 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.095372 restraints weight = 35458.230| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.07 r_work: 0.2969 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16605 Z= 0.152 Angle : 0.660 12.328 22735 Z= 0.315 Chirality : 0.046 0.422 2635 Planarity : 0.003 0.028 2760 Dihedral : 4.465 25.873 2215 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.24 % Allowed : 11.71 % Favored : 87.06 % 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: -0.36 (0.19), residues: 1965 helix: 1.41 (0.18), residues: 780 sheet: -0.47 (0.23), residues: 520 loop : -2.03 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 332 TYR 0.011 0.001 TYR B 296 PHE 0.011 0.001 PHE C 126 TRP 0.015 0.001 TRP C 176 HIS 0.004 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (16580) covalent geometry : angle 0.62605 / 0.31 (22670) SS BOND : bond 0.00786 / 0.51 ( 10) SS BOND : angle 1.33946 / 0.98 ( 20) hydrogen bonds : bond 0.06647 / 4.31 ( 806) hydrogen bonds : angle 4.68923 / 3.30 ( 2613) link_BETA1-4 : bond 0.00480 / 0.32 ( 5) link_BETA1-4 : angle 1.10447 / 0.66 ( 15) link_NAG-ASN : bond 0.00153 / 0.10 ( 10) link_NAG-ASN : angle 5.70640 / 3.75 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7859 (t0) cc_final: 0.7392 (t0) REVERT: B 66 ASP cc_start: 0.7819 (t0) cc_final: 0.7590 (t0) REVERT: B 257 ASP cc_start: 0.7245 (m-30) cc_final: 0.6726 (m-30) REVERT: C 63 MET cc_start: 0.8732 (mmm) cc_final: 0.8128 (mmm) REVERT: C 120 GLU cc_start: 0.8691 (mp0) cc_final: 0.8258 (mp0) REVERT: C 257 ASP cc_start: 0.7439 (m-30) cc_final: 0.7108 (t0) REVERT: C 345 MET cc_start: 0.7264 (mmt) cc_final: 0.7018 (mmt) REVERT: D 66 ASP cc_start: 0.7881 (t0) cc_final: 0.7421 (t0) REVERT: D 121 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6201 (ptt-90) REVERT: D 151 TYR cc_start: 0.8259 (t80) cc_final: 0.7837 (t80) REVERT: D 257 ASP cc_start: 0.7609 (m-30) cc_final: 0.7166 (t0) outliers start: 21 outliers final: 10 residues processed: 202 average time/residue: 0.4515 time to fit residues: 103.8193 Evaluate side-chains 179 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 480 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 157 optimal weight: 0.0470 chunk 87 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.113781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.091547 restraints weight = 35839.965| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.09 r_work: 0.2914 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16605 Z= 0.195 Angle : 0.697 12.437 22735 Z= 0.333 Chirality : 0.048 0.446 2635 Planarity : 0.004 0.029 2760 Dihedral : 4.732 25.906 2215 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.00 % Allowed : 11.71 % Favored : 86.29 % 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: -0.34 (0.19), residues: 1965 helix: 1.61 (0.19), residues: 760 sheet: -0.64 (0.23), residues: 520 loop : -2.00 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 441 TYR 0.013 0.002 TYR A 442 PHE 0.020 0.002 PHE B 297 TRP 0.019 0.001 TRP B 156 HIS 0.006 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (16580) covalent geometry : angle 0.66484 / 0.33 (22670) SS BOND : bond 0.00729 / 0.48 ( 10) SS BOND : angle 1.58616 / 1.11 ( 20) hydrogen bonds : bond 0.06442 / 4.18 ( 806) hydrogen bonds : angle 4.65041 / 3.27 ( 2613) link_BETA1-4 : bond 0.00372 / 0.24 ( 5) link_BETA1-4 : angle 0.92816 / 0.56 ( 15) link_NAG-ASN : bond 0.00217 / 0.14 ( 10) link_NAG-ASN : angle 5.70564 / 3.75 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.512 Fit side-chains REVERT: A 66 ASP cc_start: 0.7851 (t0) cc_final: 0.7419 (t0) REVERT: A 235 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7172 (tp) REVERT: A 297 PHE cc_start: 0.7309 (m-80) cc_final: 0.6891 (m-80) REVERT: B 66 ASP cc_start: 0.7946 (t0) cc_final: 0.7688 (t0) REVERT: B 257 ASP cc_start: 0.7382 (m-30) cc_final: 0.6910 (m-30) REVERT: C 63 MET cc_start: 0.8733 (mmm) cc_final: 0.8142 (mmm) REVERT: D 66 ASP cc_start: 0.7982 (t0) cc_final: 0.7599 (t0) REVERT: D 151 TYR cc_start: 0.8161 (t80) cc_final: 0.7826 (t80) REVERT: D 156 TRP cc_start: 0.6991 (m-90) cc_final: 0.6107 (m100) REVERT: D 207 GLU cc_start: 0.7833 (pt0) cc_final: 0.7577 (pt0) REVERT: D 257 ASP cc_start: 0.7661 (m-30) cc_final: 0.7222 (t0) REVERT: D 345 MET cc_start: 0.7494 (mmt) cc_final: 0.7155 (mmt) outliers start: 34 outliers final: 16 residues processed: 197 average time/residue: 0.4327 time to fit residues: 97.7849 Evaluate side-chains 183 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 481 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 172 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 117 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.093934 restraints weight = 45432.251| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.41 r_work: 0.2924 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16605 Z= 0.129 Angle : 0.634 11.782 22735 Z= 0.299 Chirality : 0.044 0.402 2635 Planarity : 0.003 0.030 2760 Dihedral : 4.580 25.981 2215 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.53 % Allowed : 14.06 % Favored : 84.41 % 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: -0.05 (0.19), residues: 1965 helix: 1.75 (0.19), residues: 790 sheet: -0.35 (0.24), residues: 480 loop : -1.93 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 441 TYR 0.008 0.001 TYR B 296 PHE 0.015 0.001 PHE B 297 TRP 0.024 0.001 TRP A 176 HIS 0.002 0.001 HIS D 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (16580) covalent geometry : angle 0.59967 / 0.29 (22670) SS BOND : bond 0.00803 / 0.53 ( 10) SS BOND : angle 1.73340 / 1.12 ( 20) hydrogen bonds : bond 0.05662 / 3.67 ( 806) hydrogen bonds : angle 4.40001 / 3.10 ( 2613) link_BETA1-4 : bond 0.00481 / 0.30 ( 5) link_BETA1-4 : angle 1.09841 / 0.66 ( 15) link_NAG-ASN : bond 0.00239 / 0.15 ( 10) link_NAG-ASN : angle 5.47006 / 3.59 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.511 Fit side-chains REVERT: A 66 ASP cc_start: 0.7988 (t0) cc_final: 0.7590 (t0) REVERT: A 297 PHE cc_start: 0.7252 (m-80) cc_final: 0.6946 (m-80) REVERT: B 66 ASP cc_start: 0.7984 (t0) cc_final: 0.7731 (t0) REVERT: B 257 ASP cc_start: 0.7334 (m-30) cc_final: 0.6832 (m-30) REVERT: B 441 ARG cc_start: 0.6817 (tpp80) cc_final: 0.6600 (mtt-85) REVERT: C 63 MET cc_start: 0.8721 (mmm) cc_final: 0.8114 (mmm) REVERT: C 257 ASP cc_start: 0.7409 (m-30) cc_final: 0.7055 (t0) REVERT: C 345 MET cc_start: 0.7277 (mmt) cc_final: 0.7071 (mmt) REVERT: D 151 TYR cc_start: 0.8320 (t80) cc_final: 0.8015 (t80) REVERT: D 207 GLU cc_start: 0.7701 (pt0) cc_final: 0.7436 (pt0) REVERT: D 257 ASP cc_start: 0.7664 (m-30) cc_final: 0.7180 (t0) REVERT: D 345 MET cc_start: 0.7414 (mmt) cc_final: 0.7187 (mmt) outliers start: 26 outliers final: 9 residues processed: 191 average time/residue: 0.4417 time to fit residues: 97.0561 Evaluate side-chains 173 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain E residue 481 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 179 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 108 optimal weight: 0.0370 chunk 56 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094551 restraints weight = 51283.255| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.63 r_work: 0.2942 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16605 Z= 0.123 Angle : 0.619 11.328 22735 Z= 0.292 Chirality : 0.043 0.387 2635 Planarity : 0.003 0.031 2760 Dihedral : 4.470 25.842 2215 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.29 % Allowed : 15.06 % Favored : 83.65 % 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: 0.15 (0.19), residues: 1965 helix: 1.75 (0.18), residues: 825 sheet: -0.28 (0.24), residues: 480 loop : -1.75 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 441 TYR 0.008 0.001 TYR B 296 PHE 0.014 0.001 PHE C 297 TRP 0.024 0.001 TRP A 176 HIS 0.002 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16580) covalent geometry : angle 0.58709 / 0.28 (22670) SS BOND : bond 0.00759 / 0.49 ( 10) SS BOND : angle 1.61869 / 1.07 ( 20) hydrogen bonds : bond 0.05320 / 3.44 ( 806) hydrogen bonds : angle 4.26278 / 3.00 ( 2613) link_BETA1-4 : bond 0.00478 / 0.31 ( 5) link_BETA1-4 : angle 1.09472 / 0.66 ( 15) link_NAG-ASN : bond 0.00200 / 0.13 ( 10) link_NAG-ASN : angle 5.22191 / 3.43 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.622 Fit side-chains REVERT: A 66 ASP cc_start: 0.7941 (t0) cc_final: 0.7529 (t0) REVERT: A 235 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7089 (mp) REVERT: A 297 PHE cc_start: 0.7202 (m-80) cc_final: 0.6861 (m-80) REVERT: B 66 ASP cc_start: 0.7934 (t0) cc_final: 0.7682 (t0) REVERT: B 257 ASP cc_start: 0.7293 (m-30) cc_final: 0.6797 (m-30) REVERT: C 63 MET cc_start: 0.8719 (mmm) cc_final: 0.8029 (mmm) REVERT: C 120 GLU cc_start: 0.8586 (mp0) cc_final: 0.8169 (mp0) REVERT: C 257 ASP cc_start: 0.7347 (m-30) cc_final: 0.6994 (t0) REVERT: C 345 MET cc_start: 0.7286 (mmt) cc_final: 0.7084 (mmt) REVERT: D 121 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6184 (ptt-90) REVERT: D 151 TYR cc_start: 0.8345 (t80) cc_final: 0.8054 (t80) REVERT: D 257 ASP cc_start: 0.7655 (m-30) cc_final: 0.7178 (t0) REVERT: D 345 MET cc_start: 0.7295 (mmt) cc_final: 0.7072 (mmt) REVERT: E 176 TRP cc_start: 0.7803 (m-90) cc_final: 0.7587 (m-90) outliers start: 22 outliers final: 13 residues processed: 192 average time/residue: 0.4674 time to fit residues: 102.5329 Evaluate side-chains 188 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 480 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 21 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 127 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096120 restraints weight = 45769.026| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.45 r_work: 0.2951 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16605 Z= 0.118 Angle : 0.627 13.144 22735 Z= 0.293 Chirality : 0.043 0.379 2635 Planarity : 0.003 0.031 2760 Dihedral : 4.427 25.716 2215 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.29 % Allowed : 15.82 % Favored : 82.88 % 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: 0.26 (0.19), residues: 1965 helix: 1.82 (0.18), residues: 825 sheet: -0.19 (0.24), residues: 480 loop : -1.69 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 441 TYR 0.008 0.001 TYR E 296 PHE 0.022 0.001 PHE E 297 TRP 0.031 0.001 TRP E 176 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (16580) covalent geometry : angle 0.59775 / 0.29 (22670) SS BOND : bond 0.00766 / 0.50 ( 10) SS BOND : angle 1.51652 / 1.05 ( 20) hydrogen bonds : bond 0.05074 / 3.28 ( 806) hydrogen bonds : angle 4.17667 / 2.94 ( 2613) link_BETA1-4 : bond 0.00402 / 0.26 ( 5) link_BETA1-4 : angle 1.10003 / 0.65 ( 15) link_NAG-ASN : bond 0.00258 / 0.17 ( 10) link_NAG-ASN : angle 5.09802 / 3.35 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.658 Fit side-chains REVERT: A 66 ASP cc_start: 0.7942 (t0) cc_final: 0.7562 (t0) REVERT: A 297 PHE cc_start: 0.7162 (m-80) cc_final: 0.6889 (m-80) REVERT: B 76 ILE cc_start: 0.8606 (pt) cc_final: 0.8203 (mt) REVERT: B 99 THR cc_start: 0.8837 (p) cc_final: 0.8529 (t) REVERT: B 257 ASP cc_start: 0.7243 (m-30) cc_final: 0.6757 (m-30) REVERT: C 63 MET cc_start: 0.8735 (mmm) cc_final: 0.8046 (mmm) REVERT: C 120 GLU cc_start: 0.8584 (mp0) cc_final: 0.8159 (mp0) REVERT: C 247 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6978 (mp) REVERT: C 257 ASP cc_start: 0.7324 (m-30) cc_final: 0.6977 (t0) REVERT: C 345 MET cc_start: 0.7294 (mmt) cc_final: 0.7089 (mmt) REVERT: D 121 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6197 (ptt-90) REVERT: D 151 TYR cc_start: 0.8351 (t80) cc_final: 0.8053 (t80) REVERT: D 257 ASP cc_start: 0.7666 (m-30) cc_final: 0.7219 (t0) REVERT: D 345 MET cc_start: 0.7255 (mmt) cc_final: 0.7022 (mmt) REVERT: E 207 GLU cc_start: 0.7722 (pt0) cc_final: 0.7495 (pt0) outliers start: 22 outliers final: 13 residues processed: 194 average time/residue: 0.4232 time to fit residues: 94.7608 Evaluate side-chains 190 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 301 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 88 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 ASN A 492 ASN C 75 ASN C 492 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.089775 restraints weight = 43778.505| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.37 r_work: 0.2860 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16605 Z= 0.228 Angle : 0.727 13.594 22735 Z= 0.345 Chirality : 0.049 0.449 2635 Planarity : 0.004 0.029 2760 Dihedral : 4.816 25.737 2215 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.53 % Allowed : 15.88 % Favored : 82.59 % 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: -0.11 (0.19), residues: 1965 helix: 1.72 (0.18), residues: 795 sheet: -0.64 (0.22), residues: 525 loop : -1.85 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 441 TYR 0.014 0.002 TYR C 442 PHE 0.022 0.002 PHE E 297 TRP 0.035 0.002 TRP E 176 HIS 0.007 0.002 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (16580) covalent geometry : angle 0.69743 / 0.34 (22670) SS BOND : bond 0.00737 / 0.48 ( 10) SS BOND : angle 2.03284 / 1.30 ( 20) hydrogen bonds : bond 0.06196 / 4.02 ( 806) hydrogen bonds : angle 4.50423 / 3.18 ( 2613) link_BETA1-4 : bond 0.00296 / 0.18 ( 5) link_BETA1-4 : angle 0.98922 / 0.60 ( 15) link_NAG-ASN : bond 0.00428 / 0.28 ( 10) link_NAG-ASN : angle 5.41087 / 3.55 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.626 Fit side-chains REVERT: A 257 ASP cc_start: 0.7289 (m-30) cc_final: 0.6867 (m-30) REVERT: A 297 PHE cc_start: 0.7262 (m-80) cc_final: 0.6954 (m-80) REVERT: B 257 ASP cc_start: 0.7445 (m-30) cc_final: 0.7000 (m-30) REVERT: B 441 ARG cc_start: 0.6888 (tpp80) cc_final: 0.6676 (mtt-85) REVERT: C 63 MET cc_start: 0.8707 (mmm) cc_final: 0.8038 (mmm) REVERT: C 120 GLU cc_start: 0.8614 (mp0) cc_final: 0.8234 (mp0) REVERT: C 235 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7111 (mp) REVERT: C 247 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6918 (mp) REVERT: D 121 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6374 (ptt-90) REVERT: D 151 TYR cc_start: 0.8276 (t80) cc_final: 0.7902 (t80) REVERT: D 156 TRP cc_start: 0.7032 (m-90) cc_final: 0.6199 (m100) REVERT: D 235 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7331 (mp) REVERT: D 257 ASP cc_start: 0.7556 (m-30) cc_final: 0.7238 (t0) REVERT: D 345 MET cc_start: 0.7497 (mmt) cc_final: 0.7269 (mmt) REVERT: E 207 GLU cc_start: 0.7728 (pt0) cc_final: 0.7487 (pt0) outliers start: 26 outliers final: 15 residues processed: 197 average time/residue: 0.4455 time to fit residues: 100.5917 Evaluate side-chains 190 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 480 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 70 optimal weight: 0.0570 chunk 16 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.116339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.092623 restraints weight = 57973.034| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.80 r_work: 0.2890 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16605 Z= 0.130 Angle : 0.655 13.811 22735 Z= 0.307 Chirality : 0.044 0.400 2635 Planarity : 0.003 0.031 2760 Dihedral : 4.687 25.835 2215 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.06 % Allowed : 16.94 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 1965 helix: 2.00 (0.18), residues: 790 sheet: -0.40 (0.23), residues: 490 loop : -1.95 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 441 TYR 0.011 0.001 TYR C 296 PHE 0.020 0.001 PHE E 297 TRP 0.037 0.001 TRP E 176 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16580) covalent geometry : angle 0.62500 / 0.30 (22670) SS BOND : bond 0.00743 / 0.48 ( 10) SS BOND : angle 1.51331 / 1.03 ( 20) hydrogen bonds : bond 0.05420 / 3.50 ( 806) hydrogen bonds : angle 4.31854 / 3.04 ( 2613) link_BETA1-4 : bond 0.00367 / 0.24 ( 5) link_BETA1-4 : angle 1.00823 / 0.60 ( 15) link_NAG-ASN : bond 0.00191 / 0.12 ( 10) link_NAG-ASN : angle 5.27441 / 3.46 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.573 Fit side-chains REVERT: A 257 ASP cc_start: 0.7269 (m-30) cc_final: 0.6805 (m-30) REVERT: A 297 PHE cc_start: 0.7208 (m-80) cc_final: 0.6823 (m-80) REVERT: B 257 ASP cc_start: 0.7366 (m-30) cc_final: 0.6894 (m-30) REVERT: C 63 MET cc_start: 0.8703 (mmm) cc_final: 0.8073 (mmm) REVERT: C 120 GLU cc_start: 0.8588 (mp0) cc_final: 0.8182 (mp0) REVERT: C 247 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7010 (mp) REVERT: D 121 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6192 (ptt-90) REVERT: D 151 TYR cc_start: 0.8228 (t80) cc_final: 0.7863 (t80) REVERT: D 156 TRP cc_start: 0.6975 (m-90) cc_final: 0.6077 (m100) REVERT: D 257 ASP cc_start: 0.7598 (m-30) cc_final: 0.7203 (t0) outliers start: 18 outliers final: 16 residues processed: 182 average time/residue: 0.4439 time to fit residues: 92.2277 Evaluate side-chains 186 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 480 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 172 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 175 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 147 optimal weight: 0.0010 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 0.0050 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.119738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096649 restraints weight = 45714.679| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.43 r_work: 0.2975 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16605 Z= 0.117 Angle : 0.628 13.901 22735 Z= 0.293 Chirality : 0.043 0.361 2635 Planarity : 0.003 0.031 2760 Dihedral : 4.455 25.846 2215 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.76 % Allowed : 17.41 % Favored : 81.82 % 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: 0.26 (0.19), residues: 1965 helix: 2.09 (0.18), residues: 795 sheet: -0.27 (0.24), residues: 480 loop : -1.84 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 441 TYR 0.010 0.001 TYR C 296 PHE 0.017 0.001 PHE E 297 TRP 0.030 0.001 TRP A 176 HIS 0.002 0.001 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (16580) covalent geometry : angle 0.60067 / 0.29 (22670) SS BOND : bond 0.00755 / 0.49 ( 10) SS BOND : angle 1.42238 / 0.99 ( 20) hydrogen bonds : bond 0.04797 / 3.10 ( 806) hydrogen bonds : angle 4.11295 / 2.89 ( 2613) link_BETA1-4 : bond 0.00367 / 0.21 ( 5) link_BETA1-4 : angle 1.17243 / 0.69 ( 15) link_NAG-ASN : bond 0.00317 / 0.21 ( 10) link_NAG-ASN : angle 4.93286 / 3.23 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.494 Fit side-chains REVERT: A 297 PHE cc_start: 0.6836 (m-80) cc_final: 0.6487 (m-80) REVERT: B 76 ILE cc_start: 0.8525 (pt) cc_final: 0.8163 (mt) REVERT: B 99 THR cc_start: 0.8762 (p) cc_final: 0.8449 (t) REVERT: B 257 ASP cc_start: 0.7201 (m-30) cc_final: 0.6698 (m-30) REVERT: C 63 MET cc_start: 0.8640 (mmm) cc_final: 0.7918 (mmm) REVERT: C 120 GLU cc_start: 0.8582 (mp0) cc_final: 0.8155 (mp0) REVERT: D 121 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.5990 (ptt-90) REVERT: D 151 TYR cc_start: 0.8297 (t80) cc_final: 0.7984 (t80) REVERT: D 257 ASP cc_start: 0.7546 (m-30) cc_final: 0.7125 (t0) REVERT: D 345 MET cc_start: 0.7240 (mmt) cc_final: 0.7024 (mmt) outliers start: 13 outliers final: 12 residues processed: 194 average time/residue: 0.4190 time to fit residues: 93.6768 Evaluate side-chains 184 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 480 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 132 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 38 optimal weight: 0.0870 chunk 119 optimal weight: 0.9980 chunk 123 optimal weight: 0.2980 chunk 22 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 ASN C 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097561 restraints weight = 47446.019| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.47 r_work: 0.2983 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16605 Z= 0.114 Angle : 0.631 13.838 22735 Z= 0.293 Chirality : 0.043 0.363 2635 Planarity : 0.003 0.031 2760 Dihedral : 4.405 25.815 2215 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.82 % Allowed : 17.88 % Favored : 81.29 % 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: 0.36 (0.19), residues: 1965 helix: 2.17 (0.19), residues: 795 sheet: -0.03 (0.25), residues: 430 loop : -1.84 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 441 TYR 0.011 0.001 TYR C 151 PHE 0.019 0.001 PHE C 297 TRP 0.035 0.001 TRP E 176 HIS 0.002 0.001 HIS D 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (16580) covalent geometry : angle 0.60474 / 0.29 (22670) SS BOND : bond 0.00760 / 0.49 ( 10) SS BOND : angle 1.44393 / 1.00 ( 20) hydrogen bonds : bond 0.04634 / 2.99 ( 806) hydrogen bonds : angle 4.05429 / 2.85 ( 2613) link_BETA1-4 : bond 0.00398 / 0.25 ( 5) link_BETA1-4 : angle 1.11279 / 0.66 ( 15) link_NAG-ASN : bond 0.00299 / 0.19 ( 10) link_NAG-ASN : angle 4.86760 / 3.19 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4595.22 seconds wall clock time: 79 minutes 17.89 seconds (4757.89 seconds total)