Starting phenix.real_space_refine on Sun Apr 5 18:24:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rgo_53952/04_2026/9rgo_53952.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rgo_53952/04_2026/9rgo_53952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rgo_53952/04_2026/9rgo_53952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rgo_53952/04_2026/9rgo_53952.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rgo_53952/04_2026/9rgo_53952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rgo_53952/04_2026/9rgo_53952.map" } resolution = 3.14 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= 0.009 sd= 0.113 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 80 5.16 5 Cl 1 4.86 5 C 7975 2.51 5 N 2025 2.21 5 O 2190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12271 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2454 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2454 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2454 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2454 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2454 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.61, per 1000 atoms: 0.21 Number of scatterers: 12271 At special positions: 0 Unit cell: (91.41, 93.903, 113.016, 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 1 17.00 S 80 16.00 O 2190 8.00 N 2025 7.00 C 7975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 115 " distance=2.09 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 145 " distance=2.10 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 115 " distance=2.09 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 145 " distance=2.10 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 115 " distance=2.09 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 145 " distance=2.10 Simple disulfide: pdb=" SG CYS D 69 " - pdb=" SG CYS D 115 " distance=2.09 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 145 " distance=2.10 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS E 115 " distance=2.09 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 145 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 553.6 milliseconds 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2880 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 29.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 14 through 20 removed outlier: 3.552A pdb=" N ARG A 18 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 19 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.678A pdb=" N SER A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 removed outlier: 3.688A pdb=" N ILE A 237 " --> pdb=" O SER A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 244 through 261 removed outlier: 3.527A pdb=" N LEU A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 274 through 298 removed outlier: 3.940A pdb=" N TYR A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 20 removed outlier: 3.551A pdb=" N ARG B 18 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 19 " --> pdb=" O THR B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 220 through 233 removed outlier: 3.677A pdb=" N SER B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 removed outlier: 3.688A pdb=" N ILE B 237 " --> pdb=" O SER B 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 237' Processing helix chain 'B' and resid 244 through 261 removed outlier: 3.529A pdb=" N LEU B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 274 through 298 removed outlier: 3.939A pdb=" N TYR B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 20 removed outlier: 3.551A pdb=" N ARG C 18 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU C 19 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 213 through 220 Processing helix chain 'C' and resid 220 through 233 removed outlier: 3.678A pdb=" N SER C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 removed outlier: 3.688A pdb=" N ILE C 237 " --> pdb=" O SER C 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 234 through 237' Processing helix chain 'C' and resid 244 through 261 removed outlier: 3.528A pdb=" N LEU C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 274 through 298 removed outlier: 3.939A pdb=" N TYR C 294 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 20 removed outlier: 3.550A pdb=" N ARG D 18 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 19 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 220 through 233 removed outlier: 3.677A pdb=" N SER D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 removed outlier: 3.689A pdb=" N ILE D 237 " --> pdb=" O SER D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 244 through 261 removed outlier: 3.528A pdb=" N LEU D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 274 through 298 removed outlier: 3.939A pdb=" N TYR D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 20 removed outlier: 3.551A pdb=" N ARG E 18 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU E 19 " --> pdb=" O THR E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 220 through 233 removed outlier: 3.678A pdb=" N SER E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 237 removed outlier: 3.687A pdb=" N ILE E 237 " --> pdb=" O SER E 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 237' Processing helix chain 'E' and resid 244 through 261 removed outlier: 3.527A pdb=" N LEU E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 264 No H-bonds generated for 'chain 'E' and resid 262 through 264' Processing helix chain 'E' and resid 274 through 298 removed outlier: 3.940A pdb=" N TYR E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE E 296 " --> pdb=" O ILE E 292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 76 removed outlier: 6.213A pdb=" N THR A 106 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASN A 126 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU A 108 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN A 53 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 40 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N GLN A 55 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASP A 38 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLU A 57 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU A 36 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS A 59 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER A 34 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N PHE A 61 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N ASP A 32 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 removed outlier: 7.119A pdb=" N SER A 201 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 183 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS A 210 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU A 181 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 74 through 76 removed outlier: 6.216A pdb=" N THR B 106 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASN B 126 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU B 108 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG B 124 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN B 53 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE B 40 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N GLN B 55 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASP B 38 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLU B 57 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LEU B 36 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N HIS B 59 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER B 34 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N PHE B 61 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N ASP B 32 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 91 removed outlier: 7.120A pdb=" N SER B 201 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 183 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS B 210 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU B 181 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 74 through 76 removed outlier: 6.214A pdb=" N THR C 106 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN C 126 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU C 108 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG C 124 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN C 53 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE C 40 " --> pdb=" O GLN C 53 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN C 55 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASP C 38 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLU C 57 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LEU C 36 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N HIS C 59 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N SER C 34 " --> pdb=" O HIS C 59 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N PHE C 61 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N ASP C 32 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 89 through 91 removed outlier: 7.124A pdb=" N SER C 201 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 183 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS C 210 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU C 181 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 74 through 76 removed outlier: 6.215A pdb=" N THR D 106 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASN D 126 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU D 108 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG D 124 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN D 53 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE D 40 " --> pdb=" O GLN D 53 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N GLN D 55 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASP D 38 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLU D 57 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LEU D 36 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N HIS D 59 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N SER D 34 " --> pdb=" O HIS D 59 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N PHE D 61 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N ASP D 32 " --> pdb=" O PHE D 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 89 through 91 removed outlier: 7.121A pdb=" N SER D 201 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 183 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS D 210 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU D 181 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 74 through 76 removed outlier: 6.214A pdb=" N THR E 106 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASN E 126 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU E 108 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG E 124 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS E 118 " --> pdb=" O ASP E 114 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN E 53 " --> pdb=" O PHE E 40 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE E 40 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N GLN E 55 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASP E 38 " --> pdb=" O GLN E 55 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLU E 57 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LEU E 36 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N HIS E 59 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER E 34 " --> pdb=" O HIS E 59 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N PHE E 61 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N ASP E 32 " --> pdb=" O PHE E 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 89 through 91 removed outlier: 7.115A pdb=" N SER E 201 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY E 183 " --> pdb=" O HIS E 208 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS E 210 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU E 181 " --> pdb=" O LYS E 210 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2365 1.33 - 1.45: 3672 1.45 - 1.58: 6423 1.58 - 1.70: 0 1.70 - 1.83: 120 Bond restraints: 12580 Sorted by residual: bond pdb=" CA SER A 152 " pdb=" CB SER A 152 " ideal model delta sigma weight residual 1.528 1.470 0.059 1.59e-02 3.96e+03 1.36e+01 bond pdb=" CA SER E 201 " pdb=" CB SER E 201 " ideal model delta sigma weight residual 1.528 1.479 0.050 1.35e-02 5.49e+03 1.35e+01 bond pdb=" CA SER E 152 " pdb=" CB SER E 152 " ideal model delta sigma weight residual 1.528 1.471 0.058 1.59e-02 3.96e+03 1.31e+01 bond pdb=" CA SER B 201 " pdb=" CB SER B 201 " ideal model delta sigma weight residual 1.528 1.479 0.049 1.35e-02 5.49e+03 1.30e+01 bond pdb=" CA SER D 152 " pdb=" CB SER D 152 " ideal model delta sigma weight residual 1.528 1.471 0.057 1.59e-02 3.96e+03 1.30e+01 ... (remaining 12575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 13079 1.62 - 3.23: 3133 3.23 - 4.85: 753 4.85 - 6.46: 90 6.46 - 8.08: 25 Bond angle restraints: 17080 Sorted by residual: angle pdb=" N VAL B 270 " pdb=" CA VAL B 270 " pdb=" CB VAL B 270 " ideal model delta sigma weight residual 111.21 103.15 8.06 1.40e+00 5.10e-01 3.31e+01 angle pdb=" N VAL A 270 " pdb=" CA VAL A 270 " pdb=" CB VAL A 270 " ideal model delta sigma weight residual 111.21 103.18 8.03 1.40e+00 5.10e-01 3.29e+01 angle pdb=" N VAL D 270 " pdb=" CA VAL D 270 " pdb=" CB VAL D 270 " ideal model delta sigma weight residual 111.21 103.19 8.02 1.40e+00 5.10e-01 3.29e+01 angle pdb=" N VAL E 270 " pdb=" CA VAL E 270 " pdb=" CB VAL E 270 " ideal model delta sigma weight residual 111.21 103.19 8.02 1.40e+00 5.10e-01 3.28e+01 angle pdb=" N VAL C 270 " pdb=" CA VAL C 270 " pdb=" CB VAL C 270 " ideal model delta sigma weight residual 111.21 103.21 8.00 1.40e+00 5.10e-01 3.26e+01 ... (remaining 17075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 6892 17.60 - 35.20: 493 35.20 - 52.80: 83 52.80 - 70.39: 37 70.39 - 87.99: 10 Dihedral angle restraints: 7515 sinusoidal: 3105 harmonic: 4410 Sorted by residual: dihedral pdb=" CA ASN C 25 " pdb=" C ASN C 25 " pdb=" N ASP C 26 " pdb=" CA ASP C 26 " ideal model delta harmonic sigma weight residual -180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA ASN D 25 " pdb=" C ASN D 25 " pdb=" N ASP D 26 " pdb=" CA ASP D 26 " ideal model delta harmonic sigma weight residual -180.00 -149.93 -30.07 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA ASN A 25 " pdb=" C ASN A 25 " pdb=" N ASP A 26 " pdb=" CA ASP A 26 " ideal model delta harmonic sigma weight residual -180.00 -149.96 -30.04 0 5.00e+00 4.00e-02 3.61e+01 ... (remaining 7512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1405 0.111 - 0.222: 485 0.222 - 0.333: 25 0.333 - 0.444: 0 0.444 - 0.555: 5 Chirality restraints: 1920 Sorted by residual: chirality pdb=" CA ARG E 93 " pdb=" N ARG E 93 " pdb=" C ARG E 93 " pdb=" CB ARG E 93 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CA ARG C 93 " pdb=" N ARG C 93 " pdb=" C ARG C 93 " pdb=" CB ARG C 93 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CA ARG B 93 " pdb=" N ARG B 93 " pdb=" C ARG B 93 " pdb=" CB ARG B 93 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.60e+00 ... (remaining 1917 not shown) Planarity restraints: 2140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 158 " 0.368 9.50e-02 1.11e+02 1.66e-01 1.95e+01 pdb=" NE ARG C 158 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 158 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG C 158 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 158 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 158 " -0.367 9.50e-02 1.11e+02 1.65e-01 1.94e+01 pdb=" NE ARG A 158 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 158 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG A 158 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 158 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 158 " -0.366 9.50e-02 1.11e+02 1.65e-01 1.93e+01 pdb=" NE ARG B 158 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 158 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG B 158 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 158 " -0.023 2.00e-02 2.50e+03 ... (remaining 2137 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 6426 3.01 - 3.49: 11680 3.49 - 3.96: 19509 3.96 - 4.43: 23063 4.43 - 4.90: 38409 Nonbonded interactions: 99087 Sorted by model distance: nonbonded pdb=" O PHE A 24 " pdb=" OE2 GLU E 7 " model vdw 2.543 3.040 nonbonded pdb=" OE2 GLU B 7 " pdb=" O PHE C 24 " model vdw 2.547 3.040 nonbonded pdb=" OE1 GLU A 57 " pdb=" OH TYR B 196 " model vdw 2.549 3.040 nonbonded pdb=" OE2 GLU C 7 " pdb=" O PHE D 24 " model vdw 2.555 3.040 nonbonded pdb=" OE2 GLU A 7 " pdb=" O PHE B 24 " model vdw 2.555 3.040 ... (remaining 99082 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 298) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 : 0.011 0.073 12590 Z= 0.690 Angle : 1.515 8.080 17100 Z= 0.978 Chirality : 0.098 0.555 1920 Planarity : 0.015 0.166 2140 Dihedral : 13.917 87.993 4605 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.22), residues: 1455 helix: -0.16 (0.28), residues: 285 sheet: 1.20 (0.24), residues: 400 loop : -0.49 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.004 ARG A 158 TYR 0.045 0.010 TYR D 58 PHE 0.037 0.008 PHE B 226 TRP 0.027 0.009 TRP C 279 HIS 0.014 0.005 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.01129 (12580) covalent geometry : angle 1.51273 (17080) SS BOND : bond 0.06695 ( 10) SS BOND : angle 3.04523 ( 20) hydrogen bonds : bond 0.18580 ( 475) hydrogen bonds : angle 7.20730 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.423 Fit side-chains REVERT: A 27 LYS cc_start: 0.6556 (ptpt) cc_final: 0.6215 (pttp) REVERT: A 107 ARG cc_start: 0.6919 (ttp80) cc_final: 0.5900 (mpt-90) REVERT: A 169 MET cc_start: 0.7713 (mmt) cc_final: 0.7387 (mmm) REVERT: A 212 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7571 (mm-40) REVERT: B 14 ASN cc_start: 0.5036 (t0) cc_final: 0.4834 (t0) REVERT: B 27 LYS cc_start: 0.6460 (ptpt) cc_final: 0.6138 (pttp) REVERT: B 107 ARG cc_start: 0.6787 (ttp80) cc_final: 0.5750 (tpp-160) REVERT: B 169 MET cc_start: 0.7718 (mmt) cc_final: 0.7445 (mmt) REVERT: B 272 TYR cc_start: 0.6330 (p90) cc_final: 0.5957 (p90) REVERT: C 14 ASN cc_start: 0.5432 (t0) cc_final: 0.5220 (t0) REVERT: C 27 LYS cc_start: 0.6685 (ptpt) cc_final: 0.6471 (pttp) REVERT: C 82 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7204 (mm-30) REVERT: C 107 ARG cc_start: 0.6798 (ttp80) cc_final: 0.5777 (tpp-160) REVERT: C 272 TYR cc_start: 0.6620 (p90) cc_final: 0.6217 (p90) REVERT: D 14 ASN cc_start: 0.5084 (t0) cc_final: 0.4777 (t0) REVERT: D 27 LYS cc_start: 0.6431 (ptpt) cc_final: 0.6127 (pttp) REVERT: D 107 ARG cc_start: 0.6864 (ttp80) cc_final: 0.5758 (mpt-90) REVERT: E 27 LYS cc_start: 0.6639 (ptpt) cc_final: 0.6324 (pttm) REVERT: E 82 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7349 (mm-30) REVERT: E 107 ARG cc_start: 0.6788 (ttp80) cc_final: 0.5737 (tpp-160) REVERT: E 121 MET cc_start: 0.8259 (ttp) cc_final: 0.8017 (ttt) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1101 time to fit residues: 40.8372 Evaluate side-chains 156 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 136 GLN A 188 GLN B 25 ASN B 136 GLN B 188 GLN C 25 ASN C 134 ASN C 136 GLN C 188 GLN D 25 ASN D 136 GLN D 188 GLN E 25 ASN E 188 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118958 restraints weight = 15703.341| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.33 r_work: 0.3258 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12590 Z= 0.133 Angle : 0.560 7.466 17100 Z= 0.299 Chirality : 0.046 0.147 1920 Planarity : 0.004 0.043 2140 Dihedral : 5.967 52.076 1620 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.58 % Allowed : 9.71 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.23), residues: 1455 helix: 1.22 (0.27), residues: 310 sheet: 1.34 (0.26), residues: 420 loop : -0.29 (0.26), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 162 TYR 0.014 0.001 TYR E 43 PHE 0.012 0.001 PHE E 174 TRP 0.013 0.001 TRP A 60 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00302 (12580) covalent geometry : angle 0.56041 (17080) SS BOND : bond 0.00071 ( 10) SS BOND : angle 0.55727 ( 20) hydrogen bonds : bond 0.04397 ( 475) hydrogen bonds : angle 4.94379 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.451 Fit side-chains REVERT: A 107 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7363 (tpp-160) REVERT: B 107 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7422 (tpp-160) REVERT: C 82 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7404 (mm-30) REVERT: C 107 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7356 (tpp-160) REVERT: D 14 ASN cc_start: 0.7419 (t0) cc_final: 0.7217 (t0) REVERT: D 82 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7355 (mm-30) REVERT: D 107 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7314 (tpp-160) REVERT: E 82 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7443 (mm-30) REVERT: E 107 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7393 (tpp-160) REVERT: E 169 MET cc_start: 0.7820 (mmt) cc_final: 0.7471 (mmt) outliers start: 8 outliers final: 8 residues processed: 188 average time/residue: 0.0952 time to fit residues: 26.9074 Evaluate side-chains 162 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 88 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN B 212 GLN C 212 GLN D 212 GLN E 212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104533 restraints weight = 15720.500| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.12 r_work: 0.3038 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12590 Z= 0.194 Angle : 0.585 7.647 17100 Z= 0.304 Chirality : 0.047 0.149 1920 Planarity : 0.004 0.048 2140 Dihedral : 5.686 51.928 1620 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.29 % Allowed : 10.79 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.82 (0.23), residues: 1455 helix: 1.69 (0.28), residues: 310 sheet: 1.16 (0.26), residues: 420 loop : -0.31 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 162 TYR 0.010 0.001 TYR A 80 PHE 0.012 0.001 PHE D 174 TRP 0.011 0.002 TRP B 279 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00469 (12580) covalent geometry : angle 0.58515 (17080) SS BOND : bond 0.00085 ( 10) SS BOND : angle 0.51186 ( 20) hydrogen bonds : bond 0.04324 ( 475) hydrogen bonds : angle 4.77161 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.478 Fit side-chains REVERT: A 14 ASN cc_start: 0.7127 (t0) cc_final: 0.6844 (t0) REVERT: A 107 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7399 (tpp-160) REVERT: B 10 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8877 (pp) REVERT: B 107 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7378 (tpp-160) REVERT: C 10 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8901 (pp) REVERT: C 82 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7856 (mt-10) REVERT: C 107 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7274 (tpp-160) REVERT: C 169 MET cc_start: 0.7783 (mmt) cc_final: 0.7421 (mmm) REVERT: D 10 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8891 (pp) REVERT: D 107 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7205 (tpp-160) REVERT: E 38 ASP cc_start: 0.8827 (t70) cc_final: 0.8599 (t0) REVERT: E 107 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7240 (tpp-160) outliers start: 18 outliers final: 11 residues processed: 172 average time/residue: 0.0940 time to fit residues: 24.4082 Evaluate side-chains 156 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 170 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 126 ASN A 167 ASN C 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115011 restraints weight = 15806.539| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.43 r_work: 0.3250 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12590 Z= 0.114 Angle : 0.513 7.426 17100 Z= 0.266 Chirality : 0.045 0.155 1920 Planarity : 0.004 0.049 2140 Dihedral : 5.368 52.047 1620 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.65 % Allowed : 10.22 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.97 (0.23), residues: 1455 helix: 1.97 (0.28), residues: 310 sheet: 1.26 (0.26), residues: 420 loop : -0.31 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 162 TYR 0.008 0.001 TYR A 43 PHE 0.012 0.001 PHE C 174 TRP 0.010 0.001 TRP D 60 HIS 0.002 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00262 (12580) covalent geometry : angle 0.51271 (17080) SS BOND : bond 0.00087 ( 10) SS BOND : angle 0.34390 ( 20) hydrogen bonds : bond 0.03564 ( 475) hydrogen bonds : angle 4.42607 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.419 Fit side-chains REVERT: A 14 ASN cc_start: 0.7346 (t0) cc_final: 0.7123 (t0) REVERT: A 107 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7412 (tpp-160) REVERT: A 167 ASN cc_start: 0.7201 (OUTLIER) cc_final: 0.6831 (t0) REVERT: B 10 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8899 (pp) REVERT: B 107 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7403 (tpp-160) REVERT: B 143 GLN cc_start: 0.8517 (mp10) cc_final: 0.8303 (mp10) REVERT: C 10 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8945 (pp) REVERT: C 107 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7341 (tpp-160) REVERT: C 169 MET cc_start: 0.7555 (mmt) cc_final: 0.7248 (mmm) REVERT: D 10 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8939 (pp) REVERT: D 107 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7311 (tpp-160) REVERT: E 38 ASP cc_start: 0.8577 (t70) cc_final: 0.8373 (t70) REVERT: E 107 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7340 (tpp-160) REVERT: E 143 GLN cc_start: 0.8669 (mp10) cc_final: 0.8168 (mp10) outliers start: 23 outliers final: 8 residues processed: 171 average time/residue: 0.0910 time to fit residues: 23.6349 Evaluate side-chains 152 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 88 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 126 ASN A 167 ASN C 126 ASN C 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115051 restraints weight = 15750.823| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.41 r_work: 0.3252 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12590 Z= 0.120 Angle : 0.511 7.565 17100 Z= 0.266 Chirality : 0.046 0.156 1920 Planarity : 0.004 0.052 2140 Dihedral : 5.299 52.807 1620 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.22 % Allowed : 12.01 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.98 (0.23), residues: 1455 helix: 2.09 (0.28), residues: 310 sheet: 1.21 (0.26), residues: 430 loop : -0.35 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 162 TYR 0.012 0.001 TYR B 43 PHE 0.011 0.001 PHE E 174 TRP 0.009 0.001 TRP A 60 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00281 (12580) covalent geometry : angle 0.51144 (17080) SS BOND : bond 0.00150 ( 10) SS BOND : angle 0.51278 ( 20) hydrogen bonds : bond 0.03511 ( 475) hydrogen bonds : angle 4.31784 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.298 Fit side-chains REVERT: A 14 ASN cc_start: 0.7350 (t0) cc_final: 0.7142 (t0) REVERT: A 107 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7422 (tpp-160) REVERT: B 10 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8891 (pp) REVERT: B 107 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7427 (tpp-160) REVERT: C 10 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8945 (pp) REVERT: C 107 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7343 (tpp-160) REVERT: C 143 GLN cc_start: 0.8817 (mp10) cc_final: 0.8214 (mp10) REVERT: C 169 MET cc_start: 0.7566 (mmt) cc_final: 0.7332 (mmt) REVERT: D 10 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8934 (pp) REVERT: D 14 ASN cc_start: 0.7380 (t0) cc_final: 0.7167 (t0) REVERT: D 107 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7319 (tpp-160) REVERT: E 107 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7330 (tpp-160) REVERT: E 143 GLN cc_start: 0.8699 (mp10) cc_final: 0.8180 (mp10) outliers start: 17 outliers final: 8 residues processed: 160 average time/residue: 0.0861 time to fit residues: 21.2657 Evaluate side-chains 147 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 88 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 28 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN C 126 ASN C 134 ASN D 126 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109189 restraints weight = 15581.282| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.40 r_work: 0.3214 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12590 Z= 0.117 Angle : 0.515 7.564 17100 Z= 0.267 Chirality : 0.045 0.159 1920 Planarity : 0.004 0.053 2140 Dihedral : 5.219 52.975 1620 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.15 % Allowed : 13.17 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1455 helix: 2.15 (0.28), residues: 310 sheet: 1.38 (0.27), residues: 420 loop : -0.41 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 162 TYR 0.013 0.001 TYR A 43 PHE 0.007 0.001 PHE D 123 TRP 0.008 0.001 TRP A 60 HIS 0.002 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00275 (12580) covalent geometry : angle 0.51335 (17080) SS BOND : bond 0.00213 ( 10) SS BOND : angle 1.37856 ( 20) hydrogen bonds : bond 0.03405 ( 475) hydrogen bonds : angle 4.22221 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.462 Fit side-chains REVERT: A 107 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7402 (tpp-160) REVERT: A 167 ASN cc_start: 0.7340 (t0) cc_final: 0.7058 (t0) REVERT: B 10 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8875 (pp) REVERT: B 107 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7430 (tpp-160) REVERT: B 169 MET cc_start: 0.7454 (mmt) cc_final: 0.7110 (mmm) REVERT: C 10 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8926 (pp) REVERT: C 107 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7311 (tpp-160) REVERT: C 143 GLN cc_start: 0.8775 (mp10) cc_final: 0.8185 (mp10) REVERT: C 169 MET cc_start: 0.7487 (mmt) cc_final: 0.7156 (mmm) REVERT: D 10 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8892 (pp) REVERT: D 14 ASN cc_start: 0.7389 (t0) cc_final: 0.7025 (t0) REVERT: D 107 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7290 (tpp-160) REVERT: E 10 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8886 (pp) REVERT: E 107 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7301 (tpp-160) REVERT: E 143 GLN cc_start: 0.8646 (mp10) cc_final: 0.8203 (mp10) outliers start: 16 outliers final: 8 residues processed: 157 average time/residue: 0.0841 time to fit residues: 20.4756 Evaluate side-chains 153 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 88 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 105 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN B 134 ASN C 134 ASN D 126 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.140364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113344 restraints weight = 15478.245| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.38 r_work: 0.3230 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12590 Z= 0.106 Angle : 0.506 7.592 17100 Z= 0.261 Chirality : 0.045 0.160 1920 Planarity : 0.004 0.054 2140 Dihedral : 5.120 51.715 1620 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.51 % Allowed : 13.60 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.23), residues: 1455 helix: 2.22 (0.28), residues: 310 sheet: 1.38 (0.27), residues: 420 loop : -0.43 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 162 TYR 0.011 0.001 TYR B 43 PHE 0.009 0.001 PHE C 174 TRP 0.008 0.001 TRP D 60 HIS 0.002 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00245 (12580) covalent geometry : angle 0.50414 (17080) SS BOND : bond 0.00233 ( 10) SS BOND : angle 1.43453 ( 20) hydrogen bonds : bond 0.03277 ( 475) hydrogen bonds : angle 4.10173 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.482 Fit side-chains REVERT: A 107 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7399 (tpp-160) REVERT: B 10 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8881 (pp) REVERT: B 107 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7421 (tpp-160) REVERT: B 169 MET cc_start: 0.7379 (mmt) cc_final: 0.7108 (mmt) REVERT: C 10 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8903 (pp) REVERT: C 107 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7302 (tpp-160) REVERT: C 143 GLN cc_start: 0.8764 (mp10) cc_final: 0.8225 (mp10) REVERT: C 169 MET cc_start: 0.7517 (mmt) cc_final: 0.7224 (mmm) REVERT: D 10 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8869 (pp) REVERT: D 107 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7274 (tpp-160) REVERT: D 212 GLN cc_start: 0.8165 (mm110) cc_final: 0.7935 (mm-40) REVERT: E 10 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8880 (pp) REVERT: E 107 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7293 (tpp-160) REVERT: E 143 GLN cc_start: 0.8642 (mp10) cc_final: 0.8279 (mp10) REVERT: E 169 MET cc_start: 0.7519 (mmt) cc_final: 0.7130 (mmm) outliers start: 21 outliers final: 9 residues processed: 165 average time/residue: 0.0844 time to fit residues: 21.6540 Evaluate side-chains 162 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 88 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 71 optimal weight: 0.0040 chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 134 ASN C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.139330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112120 restraints weight = 15547.061| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.39 r_work: 0.3208 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12590 Z= 0.128 Angle : 0.527 7.691 17100 Z= 0.271 Chirality : 0.046 0.165 1920 Planarity : 0.004 0.054 2140 Dihedral : 5.150 52.228 1620 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.37 % Allowed : 14.60 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.23), residues: 1455 helix: 2.14 (0.27), residues: 310 sheet: 1.31 (0.27), residues: 420 loop : -0.50 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 162 TYR 0.014 0.001 TYR B 43 PHE 0.014 0.001 PHE C 174 TRP 0.008 0.001 TRP B 279 HIS 0.002 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00305 (12580) covalent geometry : angle 0.52582 (17080) SS BOND : bond 0.00285 ( 10) SS BOND : angle 1.24371 ( 20) hydrogen bonds : bond 0.03447 ( 475) hydrogen bonds : angle 4.12441 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.559 Fit side-chains REVERT: A 107 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7415 (tpp-160) REVERT: A 176 MET cc_start: 0.8075 (mtp) cc_final: 0.7779 (ttt) REVERT: B 10 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8857 (pp) REVERT: B 107 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7409 (tpp-160) REVERT: B 169 MET cc_start: 0.7385 (mmt) cc_final: 0.7118 (mmt) REVERT: C 10 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8909 (pp) REVERT: C 107 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7293 (tpp-160) REVERT: C 169 MET cc_start: 0.7531 (mmt) cc_final: 0.7231 (mmm) REVERT: D 10 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8872 (pp) REVERT: D 107 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7287 (tpp-160) REVERT: D 212 GLN cc_start: 0.8194 (mm110) cc_final: 0.7912 (mm-40) REVERT: E 10 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8886 (pp) REVERT: E 107 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7300 (tpp-160) REVERT: E 143 GLN cc_start: 0.8601 (mp10) cc_final: 0.8165 (mp10) REVERT: E 169 MET cc_start: 0.7539 (mmt) cc_final: 0.7141 (mmm) outliers start: 19 outliers final: 8 residues processed: 154 average time/residue: 0.0849 time to fit residues: 20.2331 Evaluate side-chains 158 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain E residue 10 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 143 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 17 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN C 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118216 restraints weight = 15774.353| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.49 r_work: 0.3220 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12590 Z= 0.111 Angle : 0.518 7.659 17100 Z= 0.268 Chirality : 0.045 0.166 1920 Planarity : 0.004 0.055 2140 Dihedral : 5.074 50.595 1620 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.22 % Allowed : 15.11 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.95 (0.23), residues: 1455 helix: 2.20 (0.28), residues: 310 sheet: 1.32 (0.27), residues: 420 loop : -0.50 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 162 TYR 0.009 0.001 TYR A 43 PHE 0.014 0.001 PHE E 174 TRP 0.009 0.001 TRP D 60 HIS 0.003 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00257 (12580) covalent geometry : angle 0.51398 (17080) SS BOND : bond 0.00327 ( 10) SS BOND : angle 2.03696 ( 20) hydrogen bonds : bond 0.03270 ( 475) hydrogen bonds : angle 4.05191 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.406 Fit side-chains REVERT: A 107 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7420 (tpp-160) REVERT: A 176 MET cc_start: 0.7993 (mtp) cc_final: 0.7736 (ttt) REVERT: B 10 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8880 (pp) REVERT: B 107 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7422 (tpp-160) REVERT: B 169 MET cc_start: 0.7375 (mmt) cc_final: 0.7125 (mmt) REVERT: C 10 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8903 (pp) REVERT: C 107 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7320 (tpp-160) REVERT: C 169 MET cc_start: 0.7564 (mmt) cc_final: 0.7297 (mmm) REVERT: D 10 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8864 (pp) REVERT: D 107 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7288 (tpp-160) REVERT: D 212 GLN cc_start: 0.8182 (mm110) cc_final: 0.7921 (mm-40) REVERT: E 10 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8873 (pp) REVERT: E 107 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7289 (tpp-160) REVERT: E 143 GLN cc_start: 0.8563 (mp10) cc_final: 0.8246 (mp10) REVERT: E 169 MET cc_start: 0.7554 (mmt) cc_final: 0.7165 (mmm) outliers start: 17 outliers final: 9 residues processed: 161 average time/residue: 0.0847 time to fit residues: 21.2272 Evaluate side-chains 162 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain E residue 10 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 118 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 135 optimal weight: 0.1980 chunk 60 optimal weight: 0.0570 chunk 87 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN D 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110189 restraints weight = 15719.129| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.41 r_work: 0.3237 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12590 Z= 0.157 Angle : 0.555 7.897 17100 Z= 0.287 Chirality : 0.047 0.172 1920 Planarity : 0.004 0.055 2140 Dihedral : 5.248 52.741 1620 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.37 % Allowed : 15.54 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1455 helix: 2.11 (0.27), residues: 310 sheet: 1.00 (0.26), residues: 440 loop : -0.55 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 162 TYR 0.010 0.001 TYR C 43 PHE 0.015 0.001 PHE E 174 TRP 0.009 0.001 TRP B 279 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00378 (12580) covalent geometry : angle 0.55161 (17080) SS BOND : bond 0.00299 ( 10) SS BOND : angle 1.82142 ( 20) hydrogen bonds : bond 0.03645 ( 475) hydrogen bonds : angle 4.20497 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.448 Fit side-chains REVERT: A 107 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7370 (tpp-160) REVERT: A 176 MET cc_start: 0.8284 (mtp) cc_final: 0.8004 (ttt) REVERT: B 10 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8891 (pp) REVERT: B 107 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7402 (tpp-160) REVERT: B 169 MET cc_start: 0.7412 (mmt) cc_final: 0.7115 (mmm) REVERT: C 10 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8929 (pp) REVERT: C 107 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7328 (tpp-160) REVERT: C 169 MET cc_start: 0.7569 (mmt) cc_final: 0.7250 (mmm) REVERT: D 10 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8918 (pp) REVERT: D 107 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7309 (tpp-160) REVERT: E 10 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8906 (pp) REVERT: E 107 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7304 (tpp-160) REVERT: E 169 MET cc_start: 0.7577 (mmt) cc_final: 0.7172 (mmm) outliers start: 19 outliers final: 10 residues processed: 149 average time/residue: 0.0879 time to fit residues: 20.3894 Evaluate side-chains 155 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain E residue 10 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 0.0060 chunk 71 optimal weight: 0.6980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN C 134 ASN D 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112948 restraints weight = 15434.823| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.39 r_work: 0.3268 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12590 Z= 0.115 Angle : 0.517 7.749 17100 Z= 0.268 Chirality : 0.046 0.169 1920 Planarity : 0.004 0.055 2140 Dihedral : 5.079 50.600 1620 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.08 % Allowed : 15.76 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.88 (0.22), residues: 1455 helix: 2.20 (0.27), residues: 310 sheet: 1.25 (0.27), residues: 420 loop : -0.56 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 162 TYR 0.010 0.001 TYR D 43 PHE 0.010 0.001 PHE E 174 TRP 0.009 0.001 TRP B 279 HIS 0.002 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00270 (12580) covalent geometry : angle 0.51468 (17080) SS BOND : bond 0.00301 ( 10) SS BOND : angle 1.59011 ( 20) hydrogen bonds : bond 0.03329 ( 475) hydrogen bonds : angle 4.07439 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.97 seconds wall clock time: 38 minutes 21.49 seconds (2301.49 seconds total)