Starting phenix.real_space_refine on Sun Apr 5 19:36:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rgp_53953/04_2026/9rgp_53953.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rgp_53953/04_2026/9rgp_53953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rgp_53953/04_2026/9rgp_53953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rgp_53953/04_2026/9rgp_53953.map" model { file = "/net/cci-nas-00/data/ceres_data/9rgp_53953/04_2026/9rgp_53953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rgp_53953/04_2026/9rgp_53953.cif" } resolution = 3.65 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= 0.006 sd= 0.061 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 8240 2.51 5 N 2030 2.21 5 O 2270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 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: 12621 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2462 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2455 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 293, 2455 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 2507 Chain: "B" Number of atoms: 2462 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2455 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 293, 2455 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 2507 Chain: "C" Number of atoms: 2462 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2455 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 293, 2455 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 2507 Chain: "D" Number of atoms: 2462 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2455 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 293, 2455 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 2507 Chain: "E" Number of atoms: 2462 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2455 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 293, 2455 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 2507 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {' CL': 1, 'IVM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.94, per 1000 atoms: 0.39 Number of scatterers: 12621 At special positions: 0 Unit cell: (93.677, 94.506, 115.231, 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 2270 8.00 N 2030 7.00 C 8240 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=2.07 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=2.07 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=2.07 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=2.07 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=2.07 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: 0.90 Conformation dependent library (CDL) restraints added in 797.0 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: 2890 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 32.1% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 134 through 138 removed outlier: 4.483A pdb=" N ASN A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 213 through 220 removed outlier: 3.767A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 233 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 242 through 261 Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 274 through 298 removed outlier: 3.596A pdb=" N GLU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 134 through 138 removed outlier: 4.481A pdb=" N ASN B 137 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 213 through 220 removed outlier: 3.767A pdb=" N LEU B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 233 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 242 through 261 Processing helix chain 'B' and resid 262 through 265 Processing helix chain 'B' and resid 274 through 298 removed outlier: 3.596A pdb=" N GLU B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 134 through 138 removed outlier: 4.482A pdb=" N ASN C 137 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 213 through 220 removed outlier: 3.767A pdb=" N LEU C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 233 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 242 through 261 Processing helix chain 'C' and resid 262 through 265 Processing helix chain 'C' and resid 274 through 298 removed outlier: 3.596A pdb=" N GLU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR C 294 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 134 through 138 removed outlier: 4.481A pdb=" N ASN D 137 " --> pdb=" O ASN D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 213 through 220 removed outlier: 3.767A pdb=" N LEU D 218 " --> pdb=" O ILE D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 233 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 242 through 261 Processing helix chain 'D' and resid 262 through 265 Processing helix chain 'D' and resid 274 through 298 removed outlier: 3.597A pdb=" N GLU D 293 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 78 through 83 Processing helix chain 'E' and resid 134 through 138 removed outlier: 4.482A pdb=" N ASN E 137 " --> pdb=" O ASN E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 213 through 220 removed outlier: 3.767A pdb=" N LEU E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 233 Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 242 through 261 Processing helix chain 'E' and resid 262 through 265 Processing helix chain 'E' and resid 274 through 298 removed outlier: 3.596A pdb=" N GLU E 293 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 3.706A 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: 6.480A pdb=" N THR A 106 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASN A 126 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU A 108 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 49 " --> pdb=" O HIS A 44 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN A 53 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE A 40 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N GLN A 55 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASP A 38 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU A 57 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU A 36 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N HIS A 59 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N SER A 34 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N PHE A 61 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 9.255A 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: 7.377A pdb=" N SER A 201 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 183 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS A 210 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 5.466A 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: 6.482A pdb=" N THR B 106 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASN B 126 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU B 108 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG B 124 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 49 " --> pdb=" O HIS B 44 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN B 53 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE B 40 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLN B 55 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP B 38 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU B 57 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU B 36 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N HIS B 59 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N SER B 34 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N PHE B 61 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 9.254A 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: 7.376A pdb=" N SER B 201 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 183 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS B 210 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 5.466A 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: 6.481A pdb=" N THR C 106 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASN C 126 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 108 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG C 124 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 49 " --> pdb=" O HIS C 44 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN C 53 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE C 40 " --> pdb=" O GLN C 53 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLN C 55 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP C 38 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU C 57 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU C 36 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N HIS C 59 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER C 34 " --> pdb=" O HIS C 59 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N PHE C 61 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 9.255A 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: 7.379A pdb=" N SER C 201 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C 183 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS C 210 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 5.466A 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: 6.480A pdb=" N THR D 106 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASN D 126 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU D 108 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG D 124 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 49 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN D 53 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE D 40 " --> pdb=" O GLN D 53 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLN D 55 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP D 38 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLU D 57 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU D 36 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N HIS D 59 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N SER D 34 " --> pdb=" O HIS D 59 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N PHE D 61 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 9.255A 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: 7.380A pdb=" N SER D 201 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY D 183 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS D 210 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 5.467A 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: 6.481A pdb=" N THR E 106 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASN E 126 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU E 108 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG E 124 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS E 118 " --> pdb=" O ASP E 114 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 49 " --> pdb=" O HIS E 44 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN E 53 " --> pdb=" O PHE E 40 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE E 40 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLN E 55 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP E 38 " --> pdb=" O GLN E 55 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLU E 57 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU E 36 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N HIS E 59 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N SER E 34 " --> pdb=" O HIS E 59 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N PHE E 61 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 9.255A 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: 7.376A pdb=" N SER E 201 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY E 183 " --> pdb=" O HIS E 208 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS E 210 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU E 181 " --> pdb=" O LYS E 210 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1395 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: 1.65 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2200 1.32 - 1.45: 3766 1.45 - 1.57: 6869 1.57 - 1.70: 0 1.70 - 1.83: 120 Bond restraints: 12955 Sorted by residual: bond pdb=" C37 IVM D 301 " pdb=" C38 IVM D 301 " ideal model delta sigma weight residual 1.450 1.329 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C37 IVM B 301 " pdb=" C38 IVM B 301 " ideal model delta sigma weight residual 1.450 1.330 0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C37 IVM A 301 " pdb=" C38 IVM A 301 " ideal model delta sigma weight residual 1.450 1.330 0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C37 IVM E 301 " pdb=" C38 IVM E 301 " ideal model delta sigma weight residual 1.450 1.330 0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C37 IVM C 301 " pdb=" C38 IVM C 301 " ideal model delta sigma weight residual 1.450 1.330 0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 12950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 15368 2.30 - 4.61: 1890 4.61 - 6.91: 317 6.91 - 9.22: 40 9.22 - 11.52: 10 Bond angle restraints: 17625 Sorted by residual: angle pdb=" CA ASP C 173 " pdb=" CB ASP C 173 " pdb=" CG ASP C 173 " ideal model delta sigma weight residual 112.60 119.36 -6.76 1.00e+00 1.00e+00 4.57e+01 angle pdb=" CA ASP E 173 " pdb=" CB ASP E 173 " pdb=" CG ASP E 173 " ideal model delta sigma weight residual 112.60 119.34 -6.74 1.00e+00 1.00e+00 4.54e+01 angle pdb=" CA ASP A 173 " pdb=" CB ASP A 173 " pdb=" CG ASP A 173 " ideal model delta sigma weight residual 112.60 119.33 -6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" CA ASP B 173 " pdb=" CB ASP B 173 " pdb=" CG ASP B 173 " ideal model delta sigma weight residual 112.60 119.28 -6.68 1.00e+00 1.00e+00 4.46e+01 angle pdb=" CA ASP D 173 " pdb=" CB ASP D 173 " pdb=" CG ASP D 173 " ideal model delta sigma weight residual 112.60 119.25 -6.65 1.00e+00 1.00e+00 4.43e+01 ... (remaining 17620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.97: 7598 22.97 - 45.94: 422 45.94 - 68.91: 130 68.91 - 91.88: 55 91.88 - 114.85: 40 Dihedral angle restraints: 8245 sinusoidal: 3820 harmonic: 4425 Sorted by residual: dihedral pdb=" CA LEU D 193 " pdb=" C LEU D 193 " pdb=" N MET D 194 " pdb=" CA MET D 194 " ideal model delta harmonic sigma weight residual -180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA LEU A 193 " pdb=" C LEU A 193 " pdb=" N MET A 194 " pdb=" CA MET A 194 " ideal model delta harmonic sigma weight residual -180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA LEU C 193 " pdb=" C LEU C 193 " pdb=" N MET C 194 " pdb=" CA MET C 194 " ideal model delta harmonic sigma weight residual 180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 8242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1381 0.093 - 0.186: 553 0.186 - 0.279: 76 0.279 - 0.372: 10 0.372 - 0.465: 5 Chirality restraints: 2025 Sorted by residual: chirality pdb=" C47 IVM A 301 " pdb=" C39 IVM A 301 " pdb=" C41 IVM A 301 " pdb=" C45 IVM A 301 " both_signs ideal model delta sigma weight residual False 3.13 2.66 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" C47 IVM C 301 " pdb=" C39 IVM C 301 " pdb=" C41 IVM C 301 " pdb=" C45 IVM C 301 " both_signs ideal model delta sigma weight residual False 3.13 2.66 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" C47 IVM B 301 " pdb=" C39 IVM B 301 " pdb=" C41 IVM B 301 " pdb=" C45 IVM B 301 " both_signs ideal model delta sigma weight residual False 3.13 2.67 0.46 2.00e-01 2.50e+01 5.32e+00 ... (remaining 2022 not shown) Planarity restraints: 2170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 107 " 0.602 9.50e-02 1.11e+02 2.71e-01 4.98e+01 pdb=" NE ARG A 107 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 107 " -0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG A 107 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 107 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 107 " -0.600 9.50e-02 1.11e+02 2.70e-01 4.95e+01 pdb=" NE ARG B 107 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 107 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG B 107 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 107 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 107 " -0.598 9.50e-02 1.11e+02 2.69e-01 4.92e+01 pdb=" NE ARG C 107 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG C 107 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG C 107 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 107 " -0.033 2.00e-02 2.50e+03 ... (remaining 2167 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 20 2.52 - 3.12: 9531 3.12 - 3.71: 17900 3.71 - 4.31: 26782 4.31 - 4.90: 44245 Nonbonded interactions: 98478 Sorted by model distance: nonbonded pdb=" OG SER A 260 " pdb=" O10 IVM A 301 " model vdw 1.931 3.040 nonbonded pdb=" OG SER E 260 " pdb=" O10 IVM E 301 " model vdw 1.931 3.040 nonbonded pdb=" OG SER C 260 " pdb=" O10 IVM C 301 " model vdw 1.931 3.040 nonbonded pdb=" OG SER B 260 " pdb=" O10 IVM B 301 " model vdw 1.932 3.040 nonbonded pdb=" OG SER D 260 " pdb=" O10 IVM D 301 " model vdw 1.932 3.040 ... (remaining 98473 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 260 or resid 262 through 301)) selection = (chain 'B' and (resid 3 through 260 or resid 262 through 301)) selection = (chain 'C' and (resid 3 through 260 or resid 262 through 301)) selection = (chain 'D' and (resid 3 through 260 or resid 262 through 301)) selection = (chain 'E' and (resid 3 through 260 or resid 262 through 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.470 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 0.121 12965 Z= 0.643 Angle : 1.668 11.524 17645 Z= 1.046 Chirality : 0.098 0.465 2025 Planarity : 0.023 0.271 2170 Dihedral : 19.375 114.847 5325 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.07 % Allowed : 4.86 % Favored : 94.07 % Cbeta Deviations : 1.31 % 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: -1.45 (0.21), residues: 1455 helix: -1.62 (0.22), residues: 360 sheet: -0.85 (0.23), residues: 475 loop : -0.35 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.006 ARG C 107 TYR 0.035 0.007 TYR C 294 PHE 0.029 0.006 PHE E 123 TRP 0.036 0.010 TRP B 279 HIS 0.013 0.004 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.01065 (12955) covalent geometry : angle 1.66619 (17625) SS BOND : bond 0.05469 ( 10) SS BOND : angle 2.79118 ( 20) hydrogen bonds : bond 0.21069 ( 510) hydrogen bonds : angle 7.39651 ( 1395) *********************** 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 361 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 346 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8562 (tptt) REVERT: A 26 ASP cc_start: 0.9199 (m-30) cc_final: 0.8549 (p0) REVERT: A 35 MET cc_start: 0.8490 (ttt) cc_final: 0.8224 (ttt) REVERT: A 38 ASP cc_start: 0.8412 (t0) cc_final: 0.8161 (t70) REVERT: A 92 SER cc_start: 0.8280 (t) cc_final: 0.7898 (p) REVERT: A 293 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8149 (tp30) REVERT: B 15 LYS cc_start: 0.9124 (mtpp) cc_final: 0.8563 (tppt) REVERT: B 26 ASP cc_start: 0.9293 (m-30) cc_final: 0.8669 (p0) REVERT: B 92 SER cc_start: 0.8337 (t) cc_final: 0.7879 (p) REVERT: B 171 ARG cc_start: 0.7683 (tpp80) cc_final: 0.6668 (mtt180) REVERT: B 293 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8275 (tp30) REVERT: C 15 LYS cc_start: 0.9095 (mtpp) cc_final: 0.8547 (tptt) REVERT: C 26 ASP cc_start: 0.9284 (m-30) cc_final: 0.8634 (p0) REVERT: C 38 ASP cc_start: 0.8357 (t0) cc_final: 0.7816 (t70) REVERT: C 40 PHE cc_start: 0.8638 (t80) cc_final: 0.8102 (t80) REVERT: C 92 SER cc_start: 0.8370 (t) cc_final: 0.7906 (p) REVERT: C 293 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8103 (tp30) REVERT: D 15 LYS cc_start: 0.9052 (mtpp) cc_final: 0.8521 (tptt) REVERT: D 26 ASP cc_start: 0.9229 (m-30) cc_final: 0.8574 (p0) REVERT: D 38 ASP cc_start: 0.8451 (t0) cc_final: 0.7901 (t70) REVERT: D 40 PHE cc_start: 0.8579 (t80) cc_final: 0.8244 (t80) REVERT: D 92 SER cc_start: 0.8369 (t) cc_final: 0.7879 (p) REVERT: D 293 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8073 (tp30) REVERT: E 15 LYS cc_start: 0.9052 (mtpp) cc_final: 0.8484 (tptt) REVERT: E 26 ASP cc_start: 0.9171 (m-30) cc_final: 0.8499 (p0) REVERT: E 92 SER cc_start: 0.8415 (t) cc_final: 0.7975 (p) REVERT: E 171 ARG cc_start: 0.7730 (tpp80) cc_final: 0.6785 (mtm-85) REVERT: E 293 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8183 (tp30) outliers start: 15 outliers final: 0 residues processed: 356 average time/residue: 0.0940 time to fit residues: 50.7154 Evaluate side-chains 228 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093728 restraints weight = 53605.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099126 restraints weight = 17454.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102846 restraints weight = 9138.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105322 restraints weight = 5998.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106814 restraints weight = 4526.738| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12965 Z= 0.137 Angle : 0.727 7.910 17645 Z= 0.365 Chirality : 0.049 0.178 2025 Planarity : 0.004 0.050 2170 Dihedral : 11.540 87.525 2305 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.50 % Allowed : 15.29 % Favored : 83.21 % 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: -0.27 (0.22), residues: 1455 helix: 0.40 (0.28), residues: 345 sheet: 0.06 (0.25), residues: 420 loop : -0.52 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 93 TYR 0.019 0.002 TYR C 215 PHE 0.034 0.001 PHE A 40 TRP 0.020 0.002 TRP A 60 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00304 (12955) covalent geometry : angle 0.70707 (17625) SS BOND : bond 0.01194 ( 10) SS BOND : angle 5.13132 ( 20) hydrogen bonds : bond 0.04222 ( 510) hydrogen bonds : angle 5.29522 ( 1395) *********************** 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 325 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 304 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8603 (tppt) REVERT: A 17 ASP cc_start: 0.8158 (m-30) cc_final: 0.7606 (t70) REVERT: A 26 ASP cc_start: 0.8764 (m-30) cc_final: 0.8399 (p0) REVERT: A 92 SER cc_start: 0.8303 (t) cc_final: 0.7881 (p) REVERT: A 101 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7531 (mp0) REVERT: A 277 ASP cc_start: 0.8448 (m-30) cc_final: 0.8115 (m-30) REVERT: B 15 LYS cc_start: 0.8898 (mtpp) cc_final: 0.8626 (tppt) REVERT: B 17 ASP cc_start: 0.8189 (m-30) cc_final: 0.7612 (t70) REVERT: B 26 ASP cc_start: 0.8788 (m-30) cc_final: 0.8414 (p0) REVERT: B 29 ASP cc_start: 0.6767 (m-30) cc_final: 0.6465 (m-30) REVERT: B 92 SER cc_start: 0.7998 (t) cc_final: 0.7756 (p) REVERT: B 95 GLU cc_start: 0.8044 (tp30) cc_final: 0.7756 (tt0) REVERT: B 169 MET cc_start: 0.7247 (mmt) cc_final: 0.6921 (mmm) REVERT: B 277 ASP cc_start: 0.8598 (m-30) cc_final: 0.8363 (m-30) REVERT: C 15 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8696 (tppt) REVERT: C 17 ASP cc_start: 0.8142 (m-30) cc_final: 0.7724 (t70) REVERT: C 26 ASP cc_start: 0.8664 (m-30) cc_final: 0.8341 (p0) REVERT: C 29 ASP cc_start: 0.6872 (m-30) cc_final: 0.6565 (m-30) REVERT: C 96 ASP cc_start: 0.8470 (t0) cc_final: 0.8258 (t0) REVERT: C 101 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8044 (mp0) REVERT: D 15 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8601 (tppt) REVERT: D 17 ASP cc_start: 0.8067 (m-30) cc_final: 0.7389 (t70) REVERT: D 26 ASP cc_start: 0.8829 (m-30) cc_final: 0.8426 (p0) REVERT: D 29 ASP cc_start: 0.6588 (m-30) cc_final: 0.6328 (m-30) REVERT: D 101 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7590 (mp0) REVERT: D 277 ASP cc_start: 0.8482 (m-30) cc_final: 0.8192 (m-30) REVERT: E 15 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8616 (tppt) REVERT: E 17 ASP cc_start: 0.8052 (m-30) cc_final: 0.7590 (t70) REVERT: E 26 ASP cc_start: 0.8734 (m-30) cc_final: 0.8348 (p0) REVERT: E 38 ASP cc_start: 0.8222 (t0) cc_final: 0.7759 (t70) REVERT: E 101 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7661 (mp0) REVERT: E 277 ASP cc_start: 0.8568 (m-30) cc_final: 0.8315 (m-30) outliers start: 21 outliers final: 12 residues processed: 321 average time/residue: 0.0800 time to fit residues: 41.2562 Evaluate side-chains 219 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 19 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN B 166 GLN C 166 GLN E 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.092776 restraints weight = 69742.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098693 restraints weight = 19100.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.102788 restraints weight = 9558.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105454 restraints weight = 6164.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107220 restraints weight = 4630.092| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12965 Z= 0.123 Angle : 0.651 8.529 17645 Z= 0.323 Chirality : 0.047 0.157 2025 Planarity : 0.004 0.056 2170 Dihedral : 10.515 89.057 2305 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.64 % Allowed : 18.71 % Favored : 79.64 % 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: 0.04 (0.22), residues: 1455 helix: 0.71 (0.26), residues: 365 sheet: 0.31 (0.25), residues: 440 loop : -0.47 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 93 TYR 0.012 0.002 TYR C 43 PHE 0.020 0.001 PHE B 40 TRP 0.017 0.002 TRP A 60 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00278 (12955) covalent geometry : angle 0.63982 (17625) SS BOND : bond 0.00106 ( 10) SS BOND : angle 3.60487 ( 20) hydrogen bonds : bond 0.03745 ( 510) hydrogen bonds : angle 4.89772 ( 1395) *********************** 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 246 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8489 (tptp) REVERT: A 17 ASP cc_start: 0.8144 (m-30) cc_final: 0.7579 (t70) REVERT: A 26 ASP cc_start: 0.8712 (m-30) cc_final: 0.8360 (p0) REVERT: A 68 ASP cc_start: 0.7775 (t0) cc_final: 0.7019 (p0) REVERT: A 92 SER cc_start: 0.8168 (t) cc_final: 0.7879 (p) REVERT: A 95 GLU cc_start: 0.8327 (tp30) cc_final: 0.8101 (tp30) REVERT: B 15 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8541 (tptp) REVERT: B 17 ASP cc_start: 0.8245 (m-30) cc_final: 0.7618 (t70) REVERT: B 26 ASP cc_start: 0.8762 (m-30) cc_final: 0.8453 (p0) REVERT: B 29 ASP cc_start: 0.6721 (m-30) cc_final: 0.6520 (m-30) REVERT: B 68 ASP cc_start: 0.7762 (t0) cc_final: 0.7116 (p0) REVERT: B 92 SER cc_start: 0.8034 (t) cc_final: 0.7634 (p) REVERT: B 95 GLU cc_start: 0.8057 (tp30) cc_final: 0.7690 (tt0) REVERT: B 133 MET cc_start: 0.8588 (mmm) cc_final: 0.8379 (tpp) REVERT: C 15 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8574 (tptt) REVERT: C 17 ASP cc_start: 0.8205 (m-30) cc_final: 0.7615 (t70) REVERT: C 26 ASP cc_start: 0.8663 (m-30) cc_final: 0.8338 (p0) REVERT: C 95 GLU cc_start: 0.8356 (tp30) cc_final: 0.8145 (tp30) REVERT: C 169 MET cc_start: 0.7167 (mmt) cc_final: 0.6810 (mmm) REVERT: D 15 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8487 (tptp) REVERT: D 17 ASP cc_start: 0.8075 (m-30) cc_final: 0.7407 (t70) REVERT: D 26 ASP cc_start: 0.8797 (m-30) cc_final: 0.8431 (p0) REVERT: D 29 ASP cc_start: 0.6567 (m-30) cc_final: 0.6352 (m-30) REVERT: D 133 MET cc_start: 0.8561 (mmm) cc_final: 0.8221 (tpp) REVERT: E 15 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8440 (tptp) REVERT: E 17 ASP cc_start: 0.8010 (m-30) cc_final: 0.7416 (t70) REVERT: E 26 ASP cc_start: 0.8677 (m-30) cc_final: 0.8298 (p0) REVERT: E 38 ASP cc_start: 0.8099 (t0) cc_final: 0.7888 (t70) REVERT: E 95 GLU cc_start: 0.8291 (tp30) cc_final: 0.8086 (tp30) REVERT: E 101 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7776 (mp0) outliers start: 23 outliers final: 18 residues processed: 241 average time/residue: 0.0840 time to fit residues: 32.4638 Evaluate side-chains 218 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 249 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 71 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN B 112 GLN B 166 GLN C 112 GLN C 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093914 restraints weight = 43599.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099061 restraints weight = 15548.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102538 restraints weight = 8473.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104781 restraints weight = 5755.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106047 restraints weight = 4473.943| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12965 Z= 0.126 Angle : 0.610 8.158 17645 Z= 0.306 Chirality : 0.046 0.156 2025 Planarity : 0.004 0.060 2170 Dihedral : 9.812 89.924 2305 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.57 % Allowed : 18.36 % Favored : 79.07 % 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: 0.15 (0.22), residues: 1455 helix: 0.84 (0.26), residues: 365 sheet: 0.41 (0.25), residues: 440 loop : -0.46 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 93 TYR 0.013 0.001 TYR C 175 PHE 0.023 0.001 PHE D 40 TRP 0.016 0.001 TRP D 163 HIS 0.005 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00294 (12955) covalent geometry : angle 0.60189 (17625) SS BOND : bond 0.00052 ( 10) SS BOND : angle 3.04759 ( 20) hydrogen bonds : bond 0.03518 ( 510) hydrogen bonds : angle 4.67770 ( 1395) *********************** 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 245 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8916 (tp30) cc_final: 0.8652 (tp30) REVERT: A 15 LYS cc_start: 0.8854 (mtpp) cc_final: 0.8464 (tptp) REVERT: A 17 ASP cc_start: 0.8150 (m-30) cc_final: 0.7475 (t70) REVERT: A 26 ASP cc_start: 0.8626 (m-30) cc_final: 0.8331 (p0) REVERT: A 133 MET cc_start: 0.8267 (mtt) cc_final: 0.8020 (mmm) REVERT: B 15 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8595 (tppt) REVERT: B 17 ASP cc_start: 0.8283 (m-30) cc_final: 0.7683 (t70) REVERT: B 92 SER cc_start: 0.8022 (t) cc_final: 0.7780 (p) REVERT: B 95 GLU cc_start: 0.7962 (tp30) cc_final: 0.7516 (tt0) REVERT: C 15 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8542 (tptt) REVERT: C 17 ASP cc_start: 0.8159 (m-30) cc_final: 0.7623 (t70) REVERT: C 26 ASP cc_start: 0.8580 (m-30) cc_final: 0.8309 (p0) REVERT: C 169 MET cc_start: 0.7121 (mmt) cc_final: 0.6769 (mmm) REVERT: D 15 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8475 (tptp) REVERT: D 17 ASP cc_start: 0.8075 (m-30) cc_final: 0.7462 (t70) REVERT: D 26 ASP cc_start: 0.8693 (m-30) cc_final: 0.8394 (p0) REVERT: E 15 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8447 (tptp) REVERT: E 17 ASP cc_start: 0.8037 (m-30) cc_final: 0.7475 (t70) REVERT: E 26 ASP cc_start: 0.8587 (m-30) cc_final: 0.8235 (p0) REVERT: E 76 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8039 (tm-30) REVERT: E 133 MET cc_start: 0.8673 (tpp) cc_final: 0.8155 (tpp) outliers start: 36 outliers final: 21 residues processed: 236 average time/residue: 0.0828 time to fit residues: 30.8673 Evaluate side-chains 203 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092851 restraints weight = 46199.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097967 restraints weight = 16297.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101425 restraints weight = 8870.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103684 restraints weight = 6039.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105033 restraints weight = 4701.395| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12965 Z= 0.145 Angle : 0.615 7.217 17645 Z= 0.308 Chirality : 0.047 0.166 2025 Planarity : 0.004 0.062 2170 Dihedral : 9.845 89.889 2305 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.50 % Allowed : 19.71 % Favored : 77.79 % 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: 0.08 (0.22), residues: 1455 helix: 0.81 (0.26), residues: 365 sheet: 0.36 (0.25), residues: 440 loop : -0.51 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 171 TYR 0.013 0.002 TYR B 138 PHE 0.022 0.001 PHE B 40 TRP 0.015 0.001 TRP A 60 HIS 0.005 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00340 (12955) covalent geometry : angle 0.60879 (17625) SS BOND : bond 0.00216 ( 10) SS BOND : angle 2.59163 ( 20) hydrogen bonds : bond 0.03548 ( 510) hydrogen bonds : angle 4.66619 ( 1395) *********************** 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 231 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8852 (mtpp) cc_final: 0.8489 (tptt) REVERT: A 17 ASP cc_start: 0.8153 (m-30) cc_final: 0.7494 (t70) REVERT: A 26 ASP cc_start: 0.8607 (m-30) cc_final: 0.8317 (p0) REVERT: A 133 MET cc_start: 0.8241 (mtt) cc_final: 0.7941 (mmm) REVERT: B 15 LYS cc_start: 0.8823 (mtpp) cc_final: 0.8548 (tptp) REVERT: B 17 ASP cc_start: 0.8333 (m-30) cc_final: 0.7759 (t70) REVERT: B 92 SER cc_start: 0.8058 (t) cc_final: 0.7836 (p) REVERT: B 133 MET cc_start: 0.8788 (tpp) cc_final: 0.8564 (tpp) REVERT: B 165 ASP cc_start: 0.7905 (m-30) cc_final: 0.7327 (t0) REVERT: C 15 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8536 (tptt) REVERT: C 17 ASP cc_start: 0.8223 (m-30) cc_final: 0.7667 (t70) REVERT: D 15 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8540 (tptt) REVERT: D 17 ASP cc_start: 0.8074 (m-30) cc_final: 0.7481 (t70) REVERT: D 26 ASP cc_start: 0.8605 (m-30) cc_final: 0.8263 (p0) REVERT: D 95 GLU cc_start: 0.8146 (tp30) cc_final: 0.7807 (tt0) REVERT: D 133 MET cc_start: 0.8810 (tpp) cc_final: 0.8576 (tpp) REVERT: E 15 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8471 (tptp) REVERT: E 17 ASP cc_start: 0.8043 (m-30) cc_final: 0.7504 (t70) REVERT: E 26 ASP cc_start: 0.8575 (m-30) cc_final: 0.8262 (p0) REVERT: E 133 MET cc_start: 0.8774 (tpp) cc_final: 0.8517 (tpp) REVERT: E 203 LEU cc_start: 0.8193 (mp) cc_final: 0.7915 (mp) outliers start: 35 outliers final: 27 residues processed: 218 average time/residue: 0.0809 time to fit residues: 28.1784 Evaluate side-chains 205 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095013 restraints weight = 56958.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100405 restraints weight = 16772.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104005 restraints weight = 8449.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106386 restraints weight = 5459.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107839 restraints weight = 4100.809| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12965 Z= 0.113 Angle : 0.577 7.346 17645 Z= 0.289 Chirality : 0.045 0.199 2025 Planarity : 0.004 0.063 2170 Dihedral : 9.438 88.353 2305 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.14 % Allowed : 20.21 % Favored : 77.64 % 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: 0.21 (0.22), residues: 1455 helix: 0.92 (0.26), residues: 365 sheet: 0.53 (0.26), residues: 440 loop : -0.51 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 171 TYR 0.014 0.001 TYR D 272 PHE 0.022 0.001 PHE B 40 TRP 0.016 0.001 TRP A 60 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00261 (12955) covalent geometry : angle 0.57190 (17625) SS BOND : bond 0.00081 ( 10) SS BOND : angle 2.43113 ( 20) hydrogen bonds : bond 0.03234 ( 510) hydrogen bonds : angle 4.51776 ( 1395) *********************** 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 228 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8418 (tptt) REVERT: A 17 ASP cc_start: 0.8032 (m-30) cc_final: 0.7468 (t70) REVERT: A 133 MET cc_start: 0.8173 (mtt) cc_final: 0.7872 (mmm) REVERT: A 165 ASP cc_start: 0.7747 (m-30) cc_final: 0.7233 (t0) REVERT: B 15 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8486 (tptp) REVERT: B 17 ASP cc_start: 0.8241 (m-30) cc_final: 0.7616 (t70) REVERT: B 92 SER cc_start: 0.8076 (t) cc_final: 0.7870 (p) REVERT: B 165 ASP cc_start: 0.7921 (m-30) cc_final: 0.7367 (t0) REVERT: B 256 MET cc_start: 0.9027 (tpp) cc_final: 0.8673 (tpp) REVERT: C 15 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8518 (tptp) REVERT: C 17 ASP cc_start: 0.8146 (m-30) cc_final: 0.7607 (t70) REVERT: C 95 GLU cc_start: 0.8148 (tp30) cc_final: 0.7868 (tt0) REVERT: C 165 ASP cc_start: 0.7792 (m-30) cc_final: 0.7304 (t0) REVERT: D 15 LYS cc_start: 0.8875 (mtpp) cc_final: 0.8503 (tptt) REVERT: D 17 ASP cc_start: 0.8042 (m-30) cc_final: 0.7441 (t70) REVERT: D 256 MET cc_start: 0.9023 (tpp) cc_final: 0.8790 (ttm) REVERT: E 15 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8471 (tptt) REVERT: E 17 ASP cc_start: 0.7970 (m-30) cc_final: 0.7429 (t70) REVERT: E 26 ASP cc_start: 0.8522 (m-30) cc_final: 0.8221 (p0) REVERT: E 95 GLU cc_start: 0.8228 (tp30) cc_final: 0.7737 (tt0) REVERT: E 203 LEU cc_start: 0.8124 (mp) cc_final: 0.7789 (mp) outliers start: 30 outliers final: 22 residues processed: 215 average time/residue: 0.0826 time to fit residues: 28.1372 Evaluate side-chains 203 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094867 restraints weight = 51684.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100348 restraints weight = 16696.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104052 restraints weight = 8808.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106336 restraints weight = 5889.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108000 restraints weight = 4580.016| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12965 Z= 0.111 Angle : 0.570 6.794 17645 Z= 0.286 Chirality : 0.045 0.234 2025 Planarity : 0.004 0.064 2170 Dihedral : 9.353 87.118 2305 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.00 % Allowed : 20.00 % Favored : 78.00 % 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: 0.28 (0.22), residues: 1455 helix: 0.95 (0.26), residues: 365 sheet: 0.63 (0.26), residues: 440 loop : -0.50 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 171 TYR 0.014 0.001 TYR A 272 PHE 0.025 0.001 PHE D 40 TRP 0.014 0.001 TRP A 60 HIS 0.005 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00258 (12955) covalent geometry : angle 0.56480 (17625) SS BOND : bond 0.00073 ( 10) SS BOND : angle 2.35132 ( 20) hydrogen bonds : bond 0.03210 ( 510) hydrogen bonds : angle 4.49460 ( 1395) *********************** 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 227 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8368 (tptt) REVERT: A 17 ASP cc_start: 0.8033 (m-30) cc_final: 0.7279 (t0) REVERT: A 95 GLU cc_start: 0.8222 (tp30) cc_final: 0.7761 (tt0) REVERT: A 133 MET cc_start: 0.8164 (mtt) cc_final: 0.7859 (mmm) REVERT: B 17 ASP cc_start: 0.8228 (m-30) cc_final: 0.7606 (t70) REVERT: B 92 SER cc_start: 0.8496 (t) cc_final: 0.8066 (p) REVERT: B 133 MET cc_start: 0.8499 (tpp) cc_final: 0.6999 (mmt) REVERT: B 165 ASP cc_start: 0.7926 (m-30) cc_final: 0.7368 (t0) REVERT: B 256 MET cc_start: 0.9036 (tpp) cc_final: 0.8656 (tpp) REVERT: C 15 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8476 (tptp) REVERT: C 17 ASP cc_start: 0.8169 (m-30) cc_final: 0.7573 (t70) REVERT: C 165 ASP cc_start: 0.7873 (m-30) cc_final: 0.7340 (t0) REVERT: C 169 MET cc_start: 0.7253 (mmt) cc_final: 0.7050 (mmm) REVERT: D 15 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8462 (tptt) REVERT: D 17 ASP cc_start: 0.8065 (m-30) cc_final: 0.7408 (t70) REVERT: D 133 MET cc_start: 0.8499 (tpp) cc_final: 0.7091 (mmt) REVERT: E 15 LYS cc_start: 0.8786 (mtpp) cc_final: 0.8436 (tptt) REVERT: E 17 ASP cc_start: 0.7981 (m-30) cc_final: 0.7380 (t70) REVERT: E 26 ASP cc_start: 0.8530 (m-30) cc_final: 0.8247 (p0) REVERT: E 203 LEU cc_start: 0.8134 (mp) cc_final: 0.7775 (mp) outliers start: 28 outliers final: 26 residues processed: 218 average time/residue: 0.0795 time to fit residues: 28.0620 Evaluate side-chains 209 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 137 optimal weight: 0.0980 chunk 122 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095893 restraints weight = 51716.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.101407 restraints weight = 16709.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105183 restraints weight = 8830.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107616 restraints weight = 5903.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109115 restraints weight = 4547.302| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12965 Z= 0.105 Angle : 0.561 6.733 17645 Z= 0.281 Chirality : 0.045 0.234 2025 Planarity : 0.004 0.064 2170 Dihedral : 9.068 84.232 2305 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.36 % Allowed : 20.07 % Favored : 77.57 % 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: 0.35 (0.23), residues: 1455 helix: 0.95 (0.26), residues: 365 sheet: 0.66 (0.27), residues: 420 loop : -0.37 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 171 TYR 0.011 0.001 TYR E 43 PHE 0.022 0.001 PHE B 40 TRP 0.015 0.001 TRP A 60 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00238 (12955) covalent geometry : angle 0.55642 (17625) SS BOND : bond 0.00060 ( 10) SS BOND : angle 2.28354 ( 20) hydrogen bonds : bond 0.03195 ( 510) hydrogen bonds : angle 4.43541 ( 1395) *********************** 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 231 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8004 (m-30) cc_final: 0.7228 (t0) REVERT: A 95 GLU cc_start: 0.8213 (tp30) cc_final: 0.7817 (tt0) REVERT: A 133 MET cc_start: 0.8139 (mtt) cc_final: 0.7861 (mmm) REVERT: B 17 ASP cc_start: 0.8190 (m-30) cc_final: 0.7565 (t70) REVERT: B 92 SER cc_start: 0.8527 (t) cc_final: 0.8104 (p) REVERT: B 133 MET cc_start: 0.8441 (tpp) cc_final: 0.6984 (mmt) REVERT: B 165 ASP cc_start: 0.7935 (m-30) cc_final: 0.7345 (t0) REVERT: B 256 MET cc_start: 0.9017 (tpp) cc_final: 0.8671 (tpp) REVERT: B 294 TYR cc_start: 0.6684 (t80) cc_final: 0.6047 (t80) REVERT: C 17 ASP cc_start: 0.8157 (m-30) cc_final: 0.7526 (t70) REVERT: C 95 GLU cc_start: 0.8101 (tp30) cc_final: 0.7828 (mm-30) REVERT: C 165 ASP cc_start: 0.7824 (m-30) cc_final: 0.7322 (t0) REVERT: C 169 MET cc_start: 0.7247 (mmt) cc_final: 0.7004 (mmm) REVERT: D 15 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8409 (tptt) REVERT: D 17 ASP cc_start: 0.8048 (m-30) cc_final: 0.7394 (t70) REVERT: D 112 GLN cc_start: 0.8317 (mt0) cc_final: 0.8116 (mt0) REVERT: E 15 LYS cc_start: 0.8762 (mtpp) cc_final: 0.8428 (tptt) REVERT: E 17 ASP cc_start: 0.7983 (m-30) cc_final: 0.7428 (t70) REVERT: E 26 ASP cc_start: 0.8473 (m-30) cc_final: 0.8202 (p0) REVERT: E 95 GLU cc_start: 0.8207 (tp30) cc_final: 0.7757 (tt0) REVERT: E 203 LEU cc_start: 0.8085 (mp) cc_final: 0.7707 (mp) REVERT: E 256 MET cc_start: 0.9006 (tpp) cc_final: 0.8585 (ttm) outliers start: 33 outliers final: 28 residues processed: 221 average time/residue: 0.0827 time to fit residues: 28.9786 Evaluate side-chains 212 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 35 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093143 restraints weight = 56380.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098628 restraints weight = 17539.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102359 restraints weight = 9190.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104777 restraints weight = 6139.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106257 restraints weight = 4736.150| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12965 Z= 0.141 Angle : 0.593 6.289 17645 Z= 0.296 Chirality : 0.046 0.222 2025 Planarity : 0.004 0.065 2170 Dihedral : 9.144 84.068 2305 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.36 % Allowed : 20.43 % Favored : 77.21 % 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: 0.32 (0.23), residues: 1455 helix: 0.95 (0.26), residues: 365 sheet: 0.59 (0.27), residues: 420 loop : -0.38 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 93 TYR 0.015 0.002 TYR D 43 PHE 0.019 0.001 PHE C 40 TRP 0.012 0.001 TRP C 60 HIS 0.007 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00334 (12955) covalent geometry : angle 0.58779 (17625) SS BOND : bond 0.00150 ( 10) SS BOND : angle 2.37600 ( 20) hydrogen bonds : bond 0.03412 ( 510) hydrogen bonds : angle 4.50511 ( 1395) *********************** 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 220 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8030 (m-30) cc_final: 0.7382 (t70) REVERT: A 95 GLU cc_start: 0.8206 (tp30) cc_final: 0.7918 (tt0) REVERT: A 133 MET cc_start: 0.8175 (mtt) cc_final: 0.7880 (mmm) REVERT: B 17 ASP cc_start: 0.8304 (m-30) cc_final: 0.7705 (t70) REVERT: B 92 SER cc_start: 0.8532 (t) cc_final: 0.8128 (p) REVERT: B 133 MET cc_start: 0.8601 (tpp) cc_final: 0.7246 (mmt) REVERT: B 165 ASP cc_start: 0.7863 (m-30) cc_final: 0.7340 (t0) REVERT: B 256 MET cc_start: 0.9060 (tpp) cc_final: 0.8723 (tpp) REVERT: B 294 TYR cc_start: 0.6737 (t80) cc_final: 0.6099 (t80) REVERT: C 17 ASP cc_start: 0.8141 (m-30) cc_final: 0.7559 (t70) REVERT: C 165 ASP cc_start: 0.7748 (m-30) cc_final: 0.7333 (t0) REVERT: C 294 TYR cc_start: 0.6630 (t80) cc_final: 0.6190 (t80) REVERT: D 15 LYS cc_start: 0.8871 (mtpp) cc_final: 0.8481 (tptt) REVERT: D 17 ASP cc_start: 0.8106 (m-30) cc_final: 0.7434 (t70) REVERT: D 104 ASN cc_start: 0.8196 (m110) cc_final: 0.7582 (t0) REVERT: D 112 GLN cc_start: 0.8350 (mt0) cc_final: 0.8102 (mt0) REVERT: E 15 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8463 (tptt) REVERT: E 17 ASP cc_start: 0.7990 (m-30) cc_final: 0.7382 (t70) outliers start: 33 outliers final: 31 residues processed: 209 average time/residue: 0.0738 time to fit residues: 25.1360 Evaluate side-chains 212 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 81 optimal weight: 0.0270 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 0.0010 chunk 38 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.095235 restraints weight = 61264.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100891 restraints weight = 18075.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104777 restraints weight = 9292.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107296 restraints weight = 6129.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108815 restraints weight = 4695.634| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12965 Z= 0.104 Angle : 0.567 6.569 17645 Z= 0.284 Chirality : 0.046 0.240 2025 Planarity : 0.004 0.063 2170 Dihedral : 8.897 81.980 2305 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.57 % Allowed : 21.36 % Favored : 77.07 % 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: 0.43 (0.23), residues: 1455 helix: 0.92 (0.26), residues: 365 sheet: 0.74 (0.27), residues: 420 loop : -0.29 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 93 TYR 0.013 0.001 TYR B 272 PHE 0.027 0.001 PHE D 40 TRP 0.016 0.001 TRP A 60 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00232 (12955) covalent geometry : angle 0.56238 (17625) SS BOND : bond 0.00052 ( 10) SS BOND : angle 2.24147 ( 20) hydrogen bonds : bond 0.03317 ( 510) hydrogen bonds : angle 4.39822 ( 1395) ********************** 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 214 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7945 (m-30) cc_final: 0.7374 (t70) REVERT: A 95 GLU cc_start: 0.8104 (tp30) cc_final: 0.7772 (tt0) REVERT: A 133 MET cc_start: 0.8135 (mtt) cc_final: 0.7874 (mmm) REVERT: A 165 ASP cc_start: 0.7740 (m-30) cc_final: 0.7219 (t0) REVERT: B 17 ASP cc_start: 0.8227 (m-30) cc_final: 0.7618 (t70) REVERT: B 92 SER cc_start: 0.8570 (t) cc_final: 0.8156 (p) REVERT: B 133 MET cc_start: 0.8457 (tpp) cc_final: 0.7116 (mmt) REVERT: B 165 ASP cc_start: 0.7874 (m-30) cc_final: 0.7333 (t0) REVERT: B 171 ARG cc_start: 0.7505 (tpp80) cc_final: 0.6872 (ttm-80) REVERT: B 256 MET cc_start: 0.9024 (tpp) cc_final: 0.8701 (tpp) REVERT: B 294 TYR cc_start: 0.6711 (t80) cc_final: 0.6073 (t80) REVERT: C 17 ASP cc_start: 0.8076 (m-30) cc_final: 0.7446 (t70) REVERT: C 95 GLU cc_start: 0.8084 (tp30) cc_final: 0.7799 (mm-30) REVERT: C 165 ASP cc_start: 0.7807 (m-30) cc_final: 0.7364 (t0) REVERT: C 294 TYR cc_start: 0.6627 (t80) cc_final: 0.6179 (t80) REVERT: D 15 LYS cc_start: 0.8825 (mtpp) cc_final: 0.8420 (tptt) REVERT: D 17 ASP cc_start: 0.8073 (m-30) cc_final: 0.7436 (t70) REVERT: D 104 ASN cc_start: 0.8152 (m110) cc_final: 0.7547 (t0) REVERT: D 112 GLN cc_start: 0.8318 (mt0) cc_final: 0.8112 (mt0) REVERT: E 17 ASP cc_start: 0.7990 (m-30) cc_final: 0.7440 (t70) REVERT: E 256 MET cc_start: 0.8980 (tpp) cc_final: 0.8505 (ttm) REVERT: E 294 TYR cc_start: 0.6679 (t80) cc_final: 0.6240 (t80) outliers start: 22 outliers final: 21 residues processed: 207 average time/residue: 0.0786 time to fit residues: 26.3866 Evaluate side-chains 206 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 41 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 4 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 112 optimal weight: 0.0570 chunk 26 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 39 optimal weight: 0.0040 chunk 40 optimal weight: 7.9990 overall best weight: 1.0912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 112 GLN C 112 GLN C 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094500 restraints weight = 55005.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099944 restraints weight = 17161.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103656 restraints weight = 8987.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106079 restraints weight = 5999.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107676 restraints weight = 4632.994| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12965 Z= 0.126 Angle : 0.576 6.241 17645 Z= 0.287 Chirality : 0.046 0.237 2025 Planarity : 0.004 0.065 2170 Dihedral : 8.893 81.585 2305 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.93 % Allowed : 21.07 % Favored : 77.00 % 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: 0.41 (0.23), residues: 1455 helix: 0.94 (0.26), residues: 365 sheet: 0.71 (0.27), residues: 420 loop : -0.30 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 93 TYR 0.013 0.002 TYR E 43 PHE 0.029 0.001 PHE C 40 TRP 0.013 0.001 TRP E 60 HIS 0.005 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00297 (12955) covalent geometry : angle 0.57090 (17625) SS BOND : bond 0.00117 ( 10) SS BOND : angle 2.30815 ( 20) hydrogen bonds : bond 0.03264 ( 510) hydrogen bonds : angle 4.40417 ( 1395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2068.00 seconds wall clock time: 36 minutes 24.24 seconds (2184.24 seconds total)