Starting phenix.real_space_refine on Wed Mar 4 20:43:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ekp_31172/03_2026/7ekp_31172.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekp_31172/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ekp_31172/03_2026/7ekp_31172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekp_31172/03_2026/7ekp_31172.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ekp_31172/03_2026/7ekp_31172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekp_31172/03_2026/7ekp_31172.map" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 3.16, per 1000 atoms: 0.20 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: 1.50 Conformation dependent library (CDL) restraints added in 1.2 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: 0.54 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: 3.01 Time building geometry restraints manager: 1.98 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: 9305 17.65 - 35.31: 700 35.31 - 52.96: 165 52.96 - 70.62: 30 70.62 - 88.27: 5 Dihedral angle restraints: 10205 sinusoidal: 4360 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 10202 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: 0.02 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.830 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 13.087 88.272 6395 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 covalent geometry : bond 0.00685 (16580) covalent geometry : angle 0.75153 (22670) SS BOND : bond 0.00756 ( 10) SS BOND : angle 1.21014 ( 20) hydrogen bonds : bond 0.27372 ( 806) hydrogen bonds : angle 8.07975 ( 2613) link_BETA1-4 : bond 0.00145 ( 5) link_BETA1-4 : angle 4.13590 ( 15) link_NAG-ASN : bond 0.00347 ( 10) link_NAG-ASN : angle 6.36943 ( 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 : 0.454 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: 0.5259 time to fit residues: 139.7717 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 : 0.503 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.120017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097184 restraints weight = 44500.880| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.48 r_work: 0.2982 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 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 = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1421 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= 0.153 Angle : 0.677 12.521 22735 Z= 0.331 Chirality : 0.047 0.493 2635 Planarity : 0.004 0.030 2760 Dihedral : 6.529 38.333 2870 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.94 % Allowed : 7.12 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.18), residues: 1965 helix: 1.02 (0.18), residues: 780 sheet: 0.21 (0.25), residues: 440 loop : -2.20 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 332 TYR 0.013 0.001 TYR B 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 covalent geometry : bond 0.00307 (16580) covalent geometry : angle 0.63805 (22670) SS BOND : bond 0.00754 ( 10) SS BOND : angle 1.26255 ( 20) hydrogen bonds : bond 0.07795 ( 806) hydrogen bonds : angle 5.26424 ( 2613) link_BETA1-4 : bond 0.00355 ( 5) link_BETA1-4 : angle 1.99540 ( 15) link_NAG-ASN : bond 0.00569 ( 10) link_NAG-ASN : angle 6.07412 ( 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 212 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.620 Fit side-chains REVERT: A 66 ASP cc_start: 0.7809 (t0) cc_final: 0.7372 (t0) REVERT: A 473 MET cc_start: 0.5806 (mmt) cc_final: 0.5598 (ttt) REVERT: B 66 ASP cc_start: 0.7692 (t0) cc_final: 0.7390 (t70) REVERT: C 63 MET cc_start: 0.8707 (mmm) cc_final: 0.8150 (mmm) REVERT: C 257 ASP cc_start: 0.7394 (m-30) cc_final: 0.6934 (t0) REVERT: D 66 ASP cc_start: 0.7696 (t0) cc_final: 0.7261 (t0) REVERT: D 151 TYR cc_start: 0.8233 (t80) cc_final: 0.7796 (t80) REVERT: D 345 MET cc_start: 0.7416 (mmt) cc_final: 0.7000 (mmt) REVERT: E 176 TRP cc_start: 0.7736 (m-90) cc_final: 0.7406 (m-90) outliers start: 16 outliers final: 3 residues processed: 206 average time/residue: 0.4016 time to fit residues: 95.1129 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 : 0.511 ------------------------------------------------------------------------------- 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: 0.0060 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 0.0670 overall best weight: 0.5534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099556 restraints weight = 35310.789| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.10 r_work: 0.3031 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1939 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= 0.125 Angle : 0.635 12.176 22735 Z= 0.300 Chirality : 0.045 0.467 2635 Planarity : 0.003 0.028 2760 Dihedral : 6.174 37.299 2870 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.24 % Allowed : 11.12 % Favored : 87.65 % 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: -0.19 (0.19), residues: 1965 helix: 1.54 (0.19), residues: 780 sheet: -0.30 (0.23), residues: 515 loop : -2.00 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 332 TYR 0.009 0.001 TYR B 296 PHE 0.009 0.001 PHE D 493 TRP 0.013 0.001 TRP A 176 HIS 0.002 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00260 (16580) covalent geometry : angle 0.59532 (22670) SS BOND : bond 0.00796 ( 10) SS BOND : angle 1.23923 ( 20) hydrogen bonds : bond 0.06133 ( 806) hydrogen bonds : angle 4.52336 ( 2613) link_BETA1-4 : bond 0.00395 ( 5) link_BETA1-4 : angle 2.09138 ( 15) link_NAG-ASN : bond 0.00434 ( 10) link_NAG-ASN : angle 5.87047 ( 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 237 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.431 Fit side-chains REVERT: A 66 ASP cc_start: 0.7845 (t0) cc_final: 0.7325 (t0) REVERT: A 257 ASP cc_start: 0.6999 (m-30) cc_final: 0.6622 (t0) REVERT: B 66 ASP cc_start: 0.7766 (t0) cc_final: 0.7452 (t70) REVERT: B 235 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7242 (tp) REVERT: B 257 ASP cc_start: 0.7088 (m-30) cc_final: 0.6515 (m-30) REVERT: C 63 MET cc_start: 0.8731 (mmm) cc_final: 0.8150 (mmm) REVERT: C 257 ASP cc_start: 0.7504 (m-30) cc_final: 0.6981 (t0) REVERT: D 66 ASP cc_start: 0.7822 (t0) cc_final: 0.7414 (t0) REVERT: D 151 TYR cc_start: 0.8222 (t80) cc_final: 0.7798 (t80) REVERT: D 441 ARG cc_start: 0.6829 (tpp80) cc_final: 0.6614 (mtt-85) REVERT: E 176 TRP cc_start: 0.7714 (m-90) cc_final: 0.7443 (m-90) outliers start: 21 outliers final: 8 residues processed: 225 average time/residue: 0.4052 time to fit residues: 104.5696 Evaluate side-chains 190 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 457 CYS 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: 0.5980 chunk 25 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 162 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN C 193 ASN D 193 ASN E 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097931 restraints weight = 35657.079| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.08 r_work: 0.3013 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 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 = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2177 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= 0.127 Angle : 0.625 12.014 22735 Z= 0.295 Chirality : 0.045 0.477 2635 Planarity : 0.003 0.030 2760 Dihedral : 6.009 36.104 2870 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.53 % Allowed : 13.18 % Favored : 85.29 % 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: 0.02 (0.19), residues: 1965 helix: 1.82 (0.19), residues: 780 sheet: -0.33 (0.23), residues: 520 loop : -1.93 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 441 TYR 0.010 0.001 TYR C 296 PHE 0.014 0.001 PHE B 297 TRP 0.013 0.001 TRP B 156 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00280 (16580) covalent geometry : angle 0.58653 (22670) SS BOND : bond 0.00749 ( 10) SS BOND : angle 1.34677 ( 20) hydrogen bonds : bond 0.05579 ( 806) hydrogen bonds : angle 4.34419 ( 2613) link_BETA1-4 : bond 0.00338 ( 5) link_BETA1-4 : angle 1.92410 ( 15) link_NAG-ASN : bond 0.00275 ( 10) link_NAG-ASN : angle 5.75106 ( 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 215 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.526 Fit side-chains REVERT: A 66 ASP cc_start: 0.7956 (t0) cc_final: 0.7572 (t0) REVERT: A 297 PHE cc_start: 0.7331 (m-80) cc_final: 0.6997 (m-80) REVERT: B 66 ASP cc_start: 0.7909 (t0) cc_final: 0.7659 (t0) REVERT: B 235 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7253 (tp) REVERT: B 257 ASP cc_start: 0.7130 (m-30) cc_final: 0.6559 (m-30) REVERT: C 63 MET cc_start: 0.8766 (mmm) cc_final: 0.8201 (mmm) REVERT: C 120 GLU cc_start: 0.8651 (mp0) cc_final: 0.8226 (mp0) REVERT: C 257 ASP cc_start: 0.7379 (m-30) cc_final: 0.6987 (t0) REVERT: D 66 ASP cc_start: 0.7963 (t0) cc_final: 0.7565 (t0) REVERT: D 121 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6238 (ptt-90) REVERT: D 151 TYR cc_start: 0.8241 (t80) cc_final: 0.7831 (t80) REVERT: D 207 GLU cc_start: 0.7739 (pt0) cc_final: 0.7496 (pt0) REVERT: D 257 ASP cc_start: 0.7671 (m-30) cc_final: 0.7230 (t0) REVERT: E 176 TRP cc_start: 0.7707 (m-90) cc_final: 0.7472 (m-90) outliers start: 26 outliers final: 9 residues processed: 199 average time/residue: 0.4552 time to fit residues: 102.5605 Evaluate side-chains 187 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 182 MET 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: 1.9990 chunk 117 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 127 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.094976 restraints weight = 45653.508| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.46 r_work: 0.2951 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16605 Z= 0.144 Angle : 0.642 12.292 22735 Z= 0.301 Chirality : 0.046 0.500 2635 Planarity : 0.003 0.031 2760 Dihedral : 5.965 34.993 2870 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.94 % Allowed : 14.35 % Favored : 83.71 % 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: 0.14 (0.19), residues: 1965 helix: 2.02 (0.19), residues: 765 sheet: -0.28 (0.23), residues: 490 loop : -1.85 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 332 TYR 0.010 0.001 TYR E 296 PHE 0.021 0.001 PHE C 297 TRP 0.016 0.001 TRP B 156 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00331 (16580) covalent geometry : angle 0.60301 (22670) SS BOND : bond 0.00735 ( 10) SS BOND : angle 1.40430 ( 20) hydrogen bonds : bond 0.05548 ( 806) hydrogen bonds : angle 4.31576 ( 2613) link_BETA1-4 : bond 0.00242 ( 5) link_BETA1-4 : angle 1.83587 ( 15) link_NAG-ASN : bond 0.00139 ( 10) link_NAG-ASN : angle 5.87583 ( 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 219 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.569 Fit side-chains REVERT: A 66 ASP cc_start: 0.8001 (t0) cc_final: 0.7620 (t0) REVERT: A 176 TRP cc_start: 0.7712 (m-90) cc_final: 0.7506 (m-90) REVERT: A 235 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7219 (tp) REVERT: A 297 PHE cc_start: 0.7332 (m-80) cc_final: 0.7005 (m-80) REVERT: B 66 ASP cc_start: 0.7931 (t0) cc_final: 0.7679 (t0) REVERT: B 257 ASP cc_start: 0.7197 (m-30) cc_final: 0.6656 (m-30) REVERT: C 63 MET cc_start: 0.8744 (mmm) cc_final: 0.8163 (mmm) REVERT: C 120 GLU cc_start: 0.8733 (mp0) cc_final: 0.8297 (mp0) REVERT: C 247 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7075 (mp) REVERT: C 257 ASP cc_start: 0.7441 (m-30) cc_final: 0.7130 (t0) REVERT: D 66 ASP cc_start: 0.7991 (t0) cc_final: 0.7612 (t0) REVERT: D 75 ASN cc_start: 0.8144 (t0) cc_final: 0.7937 (t160) REVERT: D 121 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6312 (ptt-90) REVERT: D 151 TYR cc_start: 0.8403 (t80) cc_final: 0.8006 (t80) REVERT: D 207 GLU cc_start: 0.7767 (pt0) cc_final: 0.7514 (pt0) REVERT: D 257 ASP cc_start: 0.7629 (m-30) cc_final: 0.7186 (t0) REVERT: D 345 MET cc_start: 0.7455 (mmt) cc_final: 0.7194 (mmt) outliers start: 33 outliers final: 17 residues processed: 203 average time/residue: 0.4334 time to fit residues: 100.5193 Evaluate side-chains 193 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 459 GLU 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: 0.9990 chunk 192 optimal weight: 0.9990 chunk 108 optimal weight: 0.0980 chunk 56 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 102 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096576 restraints weight = 51263.290| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.66 r_work: 0.2968 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2484 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 : 0.616 12.123 22735 Z= 0.288 Chirality : 0.045 0.482 2635 Planarity : 0.003 0.030 2760 Dihedral : 5.955 35.555 2870 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.41 % Allowed : 15.59 % Favored : 83.00 % 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: 0.32 (0.19), residues: 1965 helix: 2.04 (0.18), residues: 795 sheet: -0.23 (0.23), residues: 490 loop : -1.71 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 332 TYR 0.008 0.001 TYR C 296 PHE 0.016 0.001 PHE E 297 TRP 0.014 0.001 TRP B 156 HIS 0.002 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00254 (16580) covalent geometry : angle 0.57631 (22670) SS BOND : bond 0.00742 ( 10) SS BOND : angle 1.36261 ( 20) hydrogen bonds : bond 0.05092 ( 806) hydrogen bonds : angle 4.17836 ( 2613) link_BETA1-4 : bond 0.00334 ( 5) link_BETA1-4 : angle 1.97061 ( 15) link_NAG-ASN : bond 0.00334 ( 10) link_NAG-ASN : angle 5.73917 ( 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 208 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.604 Fit side-chains REVERT: A 66 ASP cc_start: 0.7963 (t0) cc_final: 0.7599 (t0) REVERT: A 176 TRP cc_start: 0.7766 (m-90) cc_final: 0.7563 (m-90) REVERT: A 297 PHE cc_start: 0.7190 (m-80) cc_final: 0.6941 (m-80) REVERT: B 66 ASP cc_start: 0.7912 (t0) cc_final: 0.7658 (t0) REVERT: B 99 THR cc_start: 0.8832 (p) cc_final: 0.8531 (t) REVERT: B 257 ASP cc_start: 0.7227 (m-30) cc_final: 0.6750 (m-30) REVERT: C 63 MET cc_start: 0.8746 (mmm) cc_final: 0.8137 (mmm) REVERT: C 235 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7316 (mp) REVERT: C 257 ASP cc_start: 0.7312 (m-30) cc_final: 0.7000 (t0) REVERT: D 66 ASP cc_start: 0.8057 (t0) cc_final: 0.7712 (t0) REVERT: D 75 ASN cc_start: 0.8051 (t0) cc_final: 0.7816 (t160) REVERT: D 151 TYR cc_start: 0.8320 (t80) cc_final: 0.7912 (t80) REVERT: D 207 GLU cc_start: 0.7758 (pt0) cc_final: 0.7463 (pt0) REVERT: D 257 ASP cc_start: 0.7628 (m-30) cc_final: 0.7180 (t0) REVERT: D 345 MET cc_start: 0.7398 (mmt) cc_final: 0.7129 (mmt) outliers start: 24 outliers final: 13 residues processed: 193 average time/residue: 0.3984 time to fit residues: 88.4395 Evaluate side-chains 193 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 47 ASP 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 47 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain E residue 479 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 21 optimal weight: 0.0370 chunk 188 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.095623 restraints weight = 46011.394| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.44 r_work: 0.2955 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2576 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= 0.137 Angle : 0.633 12.915 22735 Z= 0.296 Chirality : 0.046 0.492 2635 Planarity : 0.003 0.030 2760 Dihedral : 5.909 36.598 2870 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.06 % Allowed : 16.29 % Favored : 82.65 % 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: 0.27 (0.19), residues: 1965 helix: 2.02 (0.19), residues: 795 sheet: -0.28 (0.23), residues: 490 loop : -1.72 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 332 TYR 0.010 0.001 TYR B 296 PHE 0.015 0.001 PHE E 297 TRP 0.016 0.001 TRP B 156 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00314 (16580) covalent geometry : angle 0.59412 (22670) SS BOND : bond 0.00751 ( 10) SS BOND : angle 1.54677 ( 20) hydrogen bonds : bond 0.05217 ( 806) hydrogen bonds : angle 4.19133 ( 2613) link_BETA1-4 : bond 0.00304 ( 5) link_BETA1-4 : angle 1.86835 ( 15) link_NAG-ASN : bond 0.00157 ( 10) link_NAG-ASN : angle 5.76373 ( 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 205 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.585 Fit side-chains REVERT: A 66 ASP cc_start: 0.7976 (t0) cc_final: 0.7662 (t0) REVERT: A 176 TRP cc_start: 0.7804 (m-90) cc_final: 0.7574 (m-90) REVERT: A 235 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7047 (mp) REVERT: A 297 PHE cc_start: 0.7154 (m-80) cc_final: 0.6804 (m-80) REVERT: B 66 ASP cc_start: 0.7872 (t0) cc_final: 0.7617 (t0) REVERT: B 257 ASP cc_start: 0.7233 (m-30) cc_final: 0.6757 (m-30) REVERT: C 63 MET cc_start: 0.8727 (mmm) cc_final: 0.8095 (mmm) REVERT: C 120 GLU cc_start: 0.8742 (mp0) cc_final: 0.8322 (mp0) REVERT: C 235 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7173 (mp) REVERT: C 257 ASP cc_start: 0.7401 (m-30) cc_final: 0.7100 (t0) REVERT: D 66 ASP cc_start: 0.8179 (t0) cc_final: 0.7879 (t0) REVERT: D 75 ASN cc_start: 0.7967 (t0) cc_final: 0.7745 (t160) REVERT: D 121 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6234 (ptt-90) REVERT: D 151 TYR cc_start: 0.8315 (t80) cc_final: 0.7927 (t80) REVERT: D 207 GLU cc_start: 0.7783 (pt0) cc_final: 0.7456 (pt0) REVERT: D 257 ASP cc_start: 0.7605 (m-30) cc_final: 0.7159 (t0) REVERT: D 345 MET cc_start: 0.7305 (mmt) cc_final: 0.7063 (mmt) outliers start: 18 outliers final: 14 residues processed: 198 average time/residue: 0.4338 time to fit residues: 97.7528 Evaluate side-chains 196 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 480 ILE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 235 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 495 GLU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 459 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 88 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094759 restraints weight = 43625.954| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.35 r_work: 0.2957 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16605 Z= 0.149 Angle : 0.661 13.427 22735 Z= 0.307 Chirality : 0.047 0.504 2635 Planarity : 0.003 0.031 2760 Dihedral : 5.938 37.650 2870 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.94 % Allowed : 15.53 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 1965 helix: 2.01 (0.19), residues: 795 sheet: -0.30 (0.23), residues: 490 loop : -1.76 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 332 TYR 0.011 0.001 TYR C 296 PHE 0.015 0.001 PHE E 297 TRP 0.021 0.001 TRP E 176 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00347 (16580) covalent geometry : angle 0.62319 (22670) SS BOND : bond 0.00730 ( 10) SS BOND : angle 1.55282 ( 20) hydrogen bonds : bond 0.05322 ( 806) hydrogen bonds : angle 4.23545 ( 2613) link_BETA1-4 : bond 0.00278 ( 5) link_BETA1-4 : angle 1.81465 ( 15) link_NAG-ASN : bond 0.00109 ( 10) link_NAG-ASN : angle 5.85386 ( 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 217 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.436 Fit side-chains REVERT: A 66 ASP cc_start: 0.8052 (t0) cc_final: 0.7700 (t0) REVERT: A 235 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7164 (mp) REVERT: A 297 PHE cc_start: 0.7177 (m-80) cc_final: 0.6803 (m-80) REVERT: B 66 ASP cc_start: 0.7978 (t0) cc_final: 0.7716 (t0) REVERT: B 257 ASP cc_start: 0.7261 (m-30) cc_final: 0.6803 (m-30) REVERT: C 63 MET cc_start: 0.8765 (mmm) cc_final: 0.8132 (mmm) REVERT: C 120 GLU cc_start: 0.8753 (mp0) cc_final: 0.8330 (mp0) REVERT: C 235 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7198 (mp) REVERT: C 257 ASP cc_start: 0.7445 (m-30) cc_final: 0.7157 (t0) REVERT: D 75 ASN cc_start: 0.8058 (t0) cc_final: 0.7825 (t160) REVERT: D 121 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6191 (ptt-90) REVERT: D 151 TYR cc_start: 0.8335 (t80) cc_final: 0.7956 (t80) REVERT: D 207 GLU cc_start: 0.7900 (pt0) cc_final: 0.7589 (pt0) REVERT: D 257 ASP cc_start: 0.7660 (m-30) cc_final: 0.7199 (t0) REVERT: D 345 MET cc_start: 0.7393 (mmt) cc_final: 0.7191 (mmt) REVERT: E 207 GLU cc_start: 0.7804 (pt0) cc_final: 0.7585 (pt0) outliers start: 33 outliers final: 23 residues processed: 202 average time/residue: 0.4447 time to fit residues: 102.1363 Evaluate side-chains 201 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 235 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 235 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 GLU 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 244 ILE Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 495 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 70 optimal weight: 0.0000 chunk 16 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 18 optimal weight: 0.0980 chunk 110 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097508 restraints weight = 57850.090| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.85 r_work: 0.2973 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16605 Z= 0.113 Angle : 0.626 13.588 22735 Z= 0.289 Chirality : 0.044 0.469 2635 Planarity : 0.003 0.032 2760 Dihedral : 5.932 39.989 2870 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.82 % Allowed : 17.18 % 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: 0.47 (0.19), residues: 1965 helix: 2.22 (0.19), residues: 795 sheet: -0.16 (0.23), residues: 490 loop : -1.70 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 121 TYR 0.010 0.001 TYR C 296 PHE 0.014 0.001 PHE C 297 TRP 0.018 0.001 TRP D 176 HIS 0.002 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00243 (16580) covalent geometry : angle 0.58850 (22670) SS BOND : bond 0.00777 ( 10) SS BOND : angle 1.45683 ( 20) hydrogen bonds : bond 0.04729 ( 806) hydrogen bonds : angle 4.07799 ( 2613) link_BETA1-4 : bond 0.00326 ( 5) link_BETA1-4 : angle 2.07345 ( 15) link_NAG-ASN : bond 0.00380 ( 10) link_NAG-ASN : angle 5.63267 ( 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 211 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.582 Fit side-chains REVERT: A 66 ASP cc_start: 0.7937 (t0) cc_final: 0.7619 (t0) REVERT: A 297 PHE cc_start: 0.7027 (m-80) cc_final: 0.6714 (m-80) REVERT: B 66 ASP cc_start: 0.7950 (t0) cc_final: 0.7702 (t0) REVERT: B 76 ILE cc_start: 0.8658 (pt) cc_final: 0.8282 (mt) REVERT: B 99 THR cc_start: 0.8819 (p) cc_final: 0.8524 (t) REVERT: B 257 ASP cc_start: 0.7216 (m-30) cc_final: 0.6743 (m-30) REVERT: C 63 MET cc_start: 0.8730 (mmm) cc_final: 0.8037 (mmm) REVERT: C 235 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7221 (mp) REVERT: C 257 ASP cc_start: 0.7329 (m-30) cc_final: 0.7011 (t0) REVERT: D 75 ASN cc_start: 0.8050 (t0) cc_final: 0.7737 (t160) REVERT: D 151 TYR cc_start: 0.8345 (t80) cc_final: 0.8012 (t80) REVERT: D 257 ASP cc_start: 0.7630 (m-30) cc_final: 0.7148 (t0) REVERT: D 345 MET cc_start: 0.7252 (mmt) cc_final: 0.7011 (mmt) outliers start: 14 outliers final: 14 residues processed: 204 average time/residue: 0.3996 time to fit residues: 93.7857 Evaluate side-chains 198 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 301 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: 1.9990 chunk 175 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 147 optimal weight: 0.0040 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 0.0570 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.4510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3469 r_free = 0.3469 target = 0.121959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098816 restraints weight = 45702.836| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.42 r_work: 0.3010 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16605 Z= 0.111 Angle : 0.622 13.782 22735 Z= 0.287 Chirality : 0.044 0.470 2635 Planarity : 0.003 0.033 2760 Dihedral : 5.865 41.026 2870 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.47 % Allowed : 17.94 % Favored : 81.59 % 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: 0.53 (0.19), residues: 1965 helix: 2.28 (0.19), residues: 795 sheet: 0.08 (0.25), residues: 440 loop : -1.74 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 332 TYR 0.009 0.001 TYR C 296 PHE 0.018 0.001 PHE D 297 TRP 0.019 0.001 TRP E 176 HIS 0.002 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00241 (16580) covalent geometry : angle 0.58489 (22670) SS BOND : bond 0.00756 ( 10) SS BOND : angle 1.62365 ( 20) hydrogen bonds : bond 0.04560 ( 806) hydrogen bonds : angle 4.02040 ( 2613) link_BETA1-4 : bond 0.00298 ( 5) link_BETA1-4 : angle 2.08022 ( 15) link_NAG-ASN : bond 0.00361 ( 10) link_NAG-ASN : angle 5.58534 ( 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 193 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.509 Fit side-chains REVERT: A 66 ASP cc_start: 0.8000 (t0) cc_final: 0.7703 (t0) REVERT: A 297 PHE cc_start: 0.6982 (m-80) cc_final: 0.6725 (m-80) REVERT: B 66 ASP cc_start: 0.8018 (t0) cc_final: 0.7767 (t0) REVERT: B 76 ILE cc_start: 0.8652 (pt) cc_final: 0.8298 (mt) REVERT: B 257 ASP cc_start: 0.7146 (m-30) cc_final: 0.6608 (m-30) REVERT: C 63 MET cc_start: 0.8736 (mmm) cc_final: 0.8033 (mmm) REVERT: C 120 GLU cc_start: 0.8703 (mp0) cc_final: 0.8251 (mp0) REVERT: C 235 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7223 (mp) REVERT: C 257 ASP cc_start: 0.7280 (m-30) cc_final: 0.6989 (t0) REVERT: D 75 ASN cc_start: 0.7990 (t0) cc_final: 0.7735 (t160) REVERT: D 121 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6167 (ptt-90) REVERT: D 151 TYR cc_start: 0.8351 (t80) cc_final: 0.7981 (t80) REVERT: D 257 ASP cc_start: 0.7616 (m-30) cc_final: 0.7163 (t0) REVERT: D 345 MET cc_start: 0.7267 (mmt) cc_final: 0.7034 (mmt) REVERT: E 76 ILE cc_start: 0.8499 (pt) cc_final: 0.8228 (mt) outliers start: 8 outliers final: 9 residues processed: 188 average time/residue: 0.4093 time to fit residues: 88.2763 Evaluate side-chains 182 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 301 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 132 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 119 optimal weight: 0.0470 chunk 123 optimal weight: 0.3980 chunk 22 optimal weight: 0.0010 chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 156 optimal weight: 0.0270 chunk 192 optimal weight: 2.9990 overall best weight: 0.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.102158 restraints weight = 46764.117| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.55 r_work: 0.3032 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16605 Z= 0.106 Angle : 0.613 13.694 22735 Z= 0.281 Chirality : 0.044 0.458 2635 Planarity : 0.003 0.034 2760 Dihedral : 5.837 43.667 2870 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.53 % Allowed : 17.88 % Favored : 81.59 % 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: 0.64 (0.19), residues: 1965 helix: 2.40 (0.19), residues: 795 sheet: -0.05 (0.24), residues: 480 loop : -1.65 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 121 TYR 0.009 0.001 TYR C 151 PHE 0.013 0.001 PHE D 297 TRP 0.018 0.001 TRP D 176 HIS 0.002 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00230 (16580) covalent geometry : angle 0.57695 (22670) SS BOND : bond 0.00770 ( 10) SS BOND : angle 1.47360 ( 20) hydrogen bonds : bond 0.04129 ( 806) hydrogen bonds : angle 3.88316 ( 2613) link_BETA1-4 : bond 0.00263 ( 5) link_BETA1-4 : angle 2.25855 ( 15) link_NAG-ASN : bond 0.00428 ( 10) link_NAG-ASN : angle 5.42552 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4386.36 seconds wall clock time: 75 minutes 37.62 seconds (4537.62 seconds total)