Starting phenix.real_space_refine on Fri Feb 6 04:34:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9swj_55309/02_2026/9swj_55309_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9swj_55309/02_2026/9swj_55309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9swj_55309/02_2026/9swj_55309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9swj_55309/02_2026/9swj_55309.map" model { file = "/net/cci-nas-00/data/ceres_data/9swj_55309/02_2026/9swj_55309_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9swj_55309/02_2026/9swj_55309_trim.cif" } resolution = 3.7 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 364 atoms to isotropic. 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 P 12 5.49 5 S 128 5.16 5 C 13860 2.51 5 N 3748 2.21 5 O 4220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21968 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2244 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 287} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3200 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 420, 3191 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 406} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 420, 3191 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 406} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3225 Chain: "A" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2244 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 287} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 3200 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 420, 3191 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 406} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 420, 3191 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 406} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3225 Chain: "E" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2244 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 287} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 3200 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 420, 3191 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 406} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 420, 3191 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 406} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3225 Chain: "G" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2244 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 287} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 3200 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 420, 3191 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 406} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 420, 3191 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 406} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3225 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLN D 460 " occ=0.61 ... (16 atoms not shown) pdb=" NE2BGLN D 460 " occ=0.39 residue: pdb=" N AGLN B 460 " occ=0.61 ... (16 atoms not shown) pdb=" NE2BGLN B 460 " occ=0.39 residue: pdb=" N AGLN F 460 " occ=0.61 ... (16 atoms not shown) pdb=" NE2BGLN F 460 " occ=0.39 residue: pdb=" N AGLN H 460 " occ=0.61 ... (16 atoms not shown) pdb=" NE2BGLN H 460 " occ=0.39 Time building chain proxies: 6.86, per 1000 atoms: 0.31 Number of scatterers: 21968 At special positions: 0 Unit cell: (130.38, 118.9, 146.78, 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) S 128 16.00 P 12 15.00 O 4220 8.00 N 3748 7.00 C 13860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.5 seconds 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5200 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 34 sheets defined 43.7% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'C' and resid 42 through 51 removed outlier: 4.661A pdb=" N GLN C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 51 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 79 Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 121 through 123 No H-bonds generated for 'chain 'C' and resid 121 through 123' Processing helix chain 'C' and resid 124 through 135 Processing helix chain 'C' and resid 148 through 161 removed outlier: 3.668A pdb=" N LYS C 158 " --> pdb=" O ARG C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.927A pdb=" N VAL C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 245 removed outlier: 3.887A pdb=" N CYS C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 274 Processing helix chain 'C' and resid 311 through 321 removed outlier: 4.262A pdb=" N ILE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 344 Processing helix chain 'D' and resid 56 through 67 Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 191 through 199 removed outlier: 4.358A pdb=" N VAL D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 203 Processing helix chain 'D' and resid 215 through 227 Processing helix chain 'D' and resid 232 through 250 Processing helix chain 'D' and resid 279 through 283 removed outlier: 4.280A pdb=" N TYR D 283 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.520A pdb=" N PHE D 289 " --> pdb=" O GLN D 285 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 291 " --> pdb=" O LYS D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 307 removed outlier: 3.556A pdb=" N ALA D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 338 Processing helix chain 'D' and resid 353 through 367 removed outlier: 3.557A pdb=" N VAL D 357 " --> pdb=" O THR D 353 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 399 removed outlier: 3.757A pdb=" N ILE D 387 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 424 Processing helix chain 'D' and resid 432 through 454 Processing helix chain 'A' and resid 42 through 51 removed outlier: 4.662A pdb=" N GLN A 48 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 51 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 79 Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 148 through 161 removed outlier: 3.667A pdb=" N LYS A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.927A pdb=" N VAL A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 245 removed outlier: 3.886A pdb=" N CYS A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 Processing helix chain 'A' and resid 311 through 321 removed outlier: 4.262A pdb=" N ILE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 344 Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 191 through 199 removed outlier: 4.357A pdb=" N VAL B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 203 Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 232 through 250 Processing helix chain 'B' and resid 279 through 283 removed outlier: 4.280A pdb=" N TYR B 283 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 removed outlier: 3.521A pdb=" N PHE B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 291 " --> pdb=" O LYS B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 removed outlier: 3.555A pdb=" N ALA B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 353 through 367 removed outlier: 3.557A pdb=" N VAL B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.757A pdb=" N ILE B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 432 through 454 Processing helix chain 'E' and resid 42 through 51 removed outlier: 4.662A pdb=" N GLN E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR E 51 " --> pdb=" O GLN E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 79 Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 124 through 135 Processing helix chain 'E' and resid 148 through 161 removed outlier: 3.668A pdb=" N LYS E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 202 through 216 removed outlier: 3.927A pdb=" N VAL E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 245 removed outlier: 3.887A pdb=" N CYS E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 Processing helix chain 'E' and resid 311 through 321 removed outlier: 4.262A pdb=" N ILE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER E 316 " --> pdb=" O LYS E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 344 Processing helix chain 'F' and resid 56 through 67 Processing helix chain 'F' and resid 79 through 90 Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 191 through 199 removed outlier: 4.356A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 203 Processing helix chain 'F' and resid 215 through 227 Processing helix chain 'F' and resid 232 through 250 Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.280A pdb=" N TYR F 283 " --> pdb=" O ASN F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 291 removed outlier: 3.521A pdb=" N PHE F 289 " --> pdb=" O GLN F 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 291 " --> pdb=" O LYS F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 removed outlier: 3.556A pdb=" N ALA F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 338 Processing helix chain 'F' and resid 353 through 367 removed outlier: 3.557A pdb=" N VAL F 357 " --> pdb=" O THR F 353 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 399 removed outlier: 3.757A pdb=" N ILE F 387 " --> pdb=" O ARG F 383 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU F 399 " --> pdb=" O VAL F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 424 Processing helix chain 'F' and resid 432 through 454 Processing helix chain 'G' and resid 42 through 51 removed outlier: 4.661A pdb=" N GLN G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR G 51 " --> pdb=" O GLN G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 79 Processing helix chain 'G' and resid 103 through 112 Processing helix chain 'G' and resid 121 through 123 No H-bonds generated for 'chain 'G' and resid 121 through 123' Processing helix chain 'G' and resid 124 through 135 Processing helix chain 'G' and resid 148 through 161 removed outlier: 3.668A pdb=" N LYS G 158 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 202 through 216 removed outlier: 3.927A pdb=" N VAL G 216 " --> pdb=" O GLN G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 245 removed outlier: 3.887A pdb=" N CYS G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 274 Processing helix chain 'G' and resid 311 through 321 removed outlier: 4.262A pdb=" N ILE G 315 " --> pdb=" O ALA G 311 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER G 316 " --> pdb=" O LYS G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 344 Processing helix chain 'H' and resid 56 through 67 Processing helix chain 'H' and resid 79 through 90 Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 191 through 199 removed outlier: 4.358A pdb=" N VAL H 195 " --> pdb=" O ASN H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 203 Processing helix chain 'H' and resid 215 through 227 Processing helix chain 'H' and resid 232 through 250 Processing helix chain 'H' and resid 279 through 283 removed outlier: 4.280A pdb=" N TYR H 283 " --> pdb=" O ASN H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 291 removed outlier: 3.521A pdb=" N PHE H 289 " --> pdb=" O GLN H 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU H 291 " --> pdb=" O LYS H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 307 removed outlier: 3.556A pdb=" N ALA H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 338 Processing helix chain 'H' and resid 353 through 367 removed outlier: 3.557A pdb=" N VAL H 357 " --> pdb=" O THR H 353 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP H 367 " --> pdb=" O LEU H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 399 removed outlier: 3.757A pdb=" N ILE H 387 " --> pdb=" O ARG H 383 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU H 399 " --> pdb=" O VAL H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 424 Processing helix chain 'H' and resid 432 through 454 Processing sheet with id=AA1, first strand: chain 'C' and resid 93 through 95 removed outlier: 7.069A pdb=" N ILE C 58 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY C 85 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N CYS C 60 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 181 through 184 removed outlier: 4.658A pdb=" N GLY C 174 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER C 221 " --> pdb=" O GLY C 194 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE C 196 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N CYS C 223 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 198 " --> pdb=" O CYS C 223 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLY C 225 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER C 200 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 255 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 74 through 77 Processing sheet with id=AA4, first strand: chain 'D' and resid 110 through 111 removed outlier: 4.127A pdb=" N LYS D 138 " --> pdb=" O CYS D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 204 through 207 removed outlier: 3.975A pdb=" N ARG D 165 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE D 169 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN D 258 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE D 171 " --> pdb=" O GLU D 256 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU D 256 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET D 173 " --> pdb=" O MET D 254 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET D 254 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP D 263 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 204 through 207 removed outlier: 3.975A pdb=" N ARG D 165 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE D 169 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN D 258 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE D 171 " --> pdb=" O GLU D 256 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU D 256 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET D 173 " --> pdb=" O MET D 254 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET D 254 " --> pdb=" O MET D 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 310 through 313 Processing sheet with id=AA8, first strand: chain 'D' and resid 318 through 322 removed outlier: 6.886A pdb=" N GLY D 319 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASN D 376 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU D 321 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG D 407 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL D 375 " --> pdb=" O ARG D 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 456 through 460 Processing sheet with id=AB1, first strand: chain 'A' and resid 93 through 95 removed outlier: 7.068A pdb=" N ILE A 58 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY A 85 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N CYS A 60 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 181 through 184 removed outlier: 4.658A pdb=" N GLY A 174 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A 221 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE A 196 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N CYS A 223 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 198 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY A 225 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER A 200 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 255 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 74 through 77 Processing sheet with id=AB4, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.126A pdb=" N LYS B 138 " --> pdb=" O CYS B 152 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 204 through 207 removed outlier: 3.975A pdb=" N ARG B 165 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE B 169 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN B 258 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE B 171 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU B 256 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N MET B 173 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET B 254 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP B 263 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 204 through 207 removed outlier: 3.975A pdb=" N ARG B 165 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE B 169 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN B 258 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE B 171 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU B 256 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N MET B 173 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET B 254 " --> pdb=" O MET B 173 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 310 through 313 Processing sheet with id=AB8, first strand: chain 'B' and resid 318 through 322 removed outlier: 6.888A pdb=" N GLY B 319 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASN B 376 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU B 321 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ARG B 407 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 375 " --> pdb=" O ARG B 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 456 through 460 Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 95 removed outlier: 7.069A pdb=" N ILE E 58 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY E 85 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N CYS E 60 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 181 through 184 removed outlier: 4.657A pdb=" N GLY E 174 " --> pdb=" O GLY E 225 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER E 221 " --> pdb=" O GLY E 194 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE E 196 " --> pdb=" O SER E 221 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N CYS E 223 " --> pdb=" O ILE E 196 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE E 198 " --> pdb=" O CYS E 223 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY E 225 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER E 200 " --> pdb=" O GLY E 225 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE E 255 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 74 through 77 Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 111 removed outlier: 4.126A pdb=" N LYS F 138 " --> pdb=" O CYS F 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 204 through 207 removed outlier: 3.975A pdb=" N ARG F 165 " --> pdb=" O GLU F 262 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE F 169 " --> pdb=" O ASN F 258 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN F 258 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE F 171 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLU F 256 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N MET F 173 " --> pdb=" O MET F 254 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET F 254 " --> pdb=" O MET F 173 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP F 263 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 204 through 207 removed outlier: 3.975A pdb=" N ARG F 165 " --> pdb=" O GLU F 262 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE F 169 " --> pdb=" O ASN F 258 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN F 258 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE F 171 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLU F 256 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N MET F 173 " --> pdb=" O MET F 254 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET F 254 " --> pdb=" O MET F 173 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 310 through 313 Processing sheet with id=AC8, first strand: chain 'F' and resid 318 through 322 removed outlier: 6.887A pdb=" N GLY F 319 " --> pdb=" O LEU F 374 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASN F 376 " --> pdb=" O GLY F 319 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU F 321 " --> pdb=" O ASN F 376 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG F 407 " --> pdb=" O ILE F 373 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL F 375 " --> pdb=" O ARG F 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 93 through 95 removed outlier: 7.069A pdb=" N ILE G 58 " --> pdb=" O VAL G 83 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY G 85 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N CYS G 60 " --> pdb=" O GLY G 85 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 181 through 184 removed outlier: 4.658A pdb=" N GLY G 174 " --> pdb=" O GLY G 225 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER G 221 " --> pdb=" O GLY G 194 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE G 196 " --> pdb=" O SER G 221 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N CYS G 223 " --> pdb=" O ILE G 196 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE G 198 " --> pdb=" O CYS G 223 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLY G 225 " --> pdb=" O ILE G 198 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER G 200 " --> pdb=" O GLY G 225 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G 255 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AD3, first strand: chain 'H' and resid 110 through 111 removed outlier: 4.126A pdb=" N LYS H 138 " --> pdb=" O CYS H 152 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 204 through 207 removed outlier: 3.975A pdb=" N ARG H 165 " --> pdb=" O GLU H 262 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE H 169 " --> pdb=" O ASN H 258 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN H 258 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE H 171 " --> pdb=" O GLU H 256 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU H 256 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N MET H 173 " --> pdb=" O MET H 254 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET H 254 " --> pdb=" O MET H 173 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP H 263 " --> pdb=" O ALA H 267 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA H 267 " --> pdb=" O ASP H 263 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 204 through 207 removed outlier: 3.975A pdb=" N ARG H 165 " --> pdb=" O GLU H 262 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE H 169 " --> pdb=" O ASN H 258 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN H 258 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE H 171 " --> pdb=" O GLU H 256 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU H 256 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N MET H 173 " --> pdb=" O MET H 254 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET H 254 " --> pdb=" O MET H 173 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 310 through 313 Processing sheet with id=AD7, first strand: chain 'H' and resid 318 through 322 removed outlier: 6.887A pdb=" N GLY H 319 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASN H 376 " --> pdb=" O GLY H 319 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU H 321 " --> pdb=" O ASN H 376 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ARG H 407 " --> pdb=" O ILE H 373 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL H 375 " --> pdb=" O ARG H 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 1164 hydrogen bonds defined for protein. 3192 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: 4.91 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7317 1.34 - 1.46: 4198 1.46 - 1.58: 10581 1.58 - 1.70: 20 1.70 - 1.81: 204 Bond restraints: 22320 Sorted by residual: bond pdb=" O3B COA G 401 " pdb=" P3B COA G 401 " ideal model delta sigma weight residual 1.683 1.610 0.073 2.00e-02 2.50e+03 1.31e+01 bond pdb=" O3B COA E 401 " pdb=" P3B COA E 401 " ideal model delta sigma weight residual 1.683 1.610 0.073 2.00e-02 2.50e+03 1.31e+01 bond pdb=" O3B COA A 401 " pdb=" P3B COA A 401 " ideal model delta sigma weight residual 1.683 1.612 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O3B COA C 401 " pdb=" P3B COA C 401 " ideal model delta sigma weight residual 1.683 1.612 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O3A COA E 401 " pdb=" P2A COA E 401 " ideal model delta sigma weight residual 1.632 1.599 0.033 2.00e-02 2.50e+03 2.73e+00 ... (remaining 22315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 29355 1.85 - 3.70: 705 3.70 - 5.55: 84 5.55 - 7.40: 8 7.40 - 9.25: 8 Bond angle restraints: 30160 Sorted by residual: angle pdb=" N VAL F 413 " pdb=" CA VAL F 413 " pdb=" C VAL F 413 " ideal model delta sigma weight residual 111.90 107.67 4.23 8.10e-01 1.52e+00 2.73e+01 angle pdb=" N VAL H 413 " pdb=" CA VAL H 413 " pdb=" C VAL H 413 " ideal model delta sigma weight residual 111.90 107.69 4.21 8.10e-01 1.52e+00 2.70e+01 angle pdb=" N VAL D 413 " pdb=" CA VAL D 413 " pdb=" C VAL D 413 " ideal model delta sigma weight residual 111.90 107.69 4.21 8.10e-01 1.52e+00 2.70e+01 angle pdb=" N VAL B 413 " pdb=" CA VAL B 413 " pdb=" C VAL B 413 " ideal model delta sigma weight residual 111.90 107.73 4.17 8.10e-01 1.52e+00 2.65e+01 angle pdb=" C LEU B 374 " pdb=" N VAL B 375 " pdb=" CA VAL B 375 " ideal model delta sigma weight residual 122.43 118.06 4.37 1.26e+00 6.30e-01 1.20e+01 ... (remaining 30155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12340 17.94 - 35.88: 1041 35.88 - 53.81: 195 53.81 - 71.75: 80 71.75 - 89.69: 40 Dihedral angle restraints: 13696 sinusoidal: 5528 harmonic: 8168 Sorted by residual: dihedral pdb=" CA ILE C 176 " pdb=" C ILE C 176 " pdb=" N ASN C 177 " pdb=" CA ASN C 177 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ILE G 176 " pdb=" C ILE G 176 " pdb=" N ASN G 177 " pdb=" CA ASN G 177 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ILE E 176 " pdb=" C ILE E 176 " pdb=" N ASN E 177 " pdb=" CA ASN E 177 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 13693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2299 0.039 - 0.079: 806 0.079 - 0.118: 272 0.118 - 0.158: 59 0.158 - 0.197: 12 Chirality restraints: 3448 Sorted by residual: chirality pdb=" C2B COA A 401 " pdb=" C1B COA A 401 " pdb=" C3B COA A 401 " pdb=" O2B COA A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" C2B COA E 401 " pdb=" C1B COA E 401 " pdb=" C3B COA E 401 " pdb=" O2B COA E 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" C2B COA G 401 " pdb=" C1B COA G 401 " pdb=" C3B COA G 401 " pdb=" O2B COA G 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-01 2.50e+01 9.67e-01 ... (remaining 3445 not shown) Planarity restraints: 3904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P COA E 401 " 0.355 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C9P COA E 401 " -0.099 2.00e-02 2.50e+03 pdb=" CAP COA E 401 " 0.145 2.00e-02 2.50e+03 pdb=" N8P COA E 401 " -0.536 2.00e-02 2.50e+03 pdb=" O9P COA E 401 " 0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P COA C 401 " -0.356 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C9P COA C 401 " 0.099 2.00e-02 2.50e+03 pdb=" CAP COA C 401 " -0.145 2.00e-02 2.50e+03 pdb=" N8P COA C 401 " 0.535 2.00e-02 2.50e+03 pdb=" O9P COA C 401 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P COA A 401 " -0.355 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C9P COA A 401 " 0.098 2.00e-02 2.50e+03 pdb=" CAP COA A 401 " -0.144 2.00e-02 2.50e+03 pdb=" N8P COA A 401 " 0.535 2.00e-02 2.50e+03 pdb=" O9P COA A 401 " -0.133 2.00e-02 2.50e+03 ... (remaining 3901 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 92 2.40 - 3.03: 13377 3.03 - 3.65: 34014 3.65 - 4.28: 48100 4.28 - 4.90: 81381 Nonbonded interactions: 176964 Sorted by model distance: nonbonded pdb=" OG1 THR A 64 " pdb=" O7A COA A 401 " model vdw 1.776 3.040 nonbonded pdb=" OG1 THR G 64 " pdb=" O7A COA G 401 " model vdw 1.777 3.040 nonbonded pdb=" OG1 THR E 64 " pdb=" O7A COA E 401 " model vdw 1.778 3.040 nonbonded pdb=" OG1 THR C 64 " pdb=" O7A COA C 401 " model vdw 1.956 3.040 nonbonded pdb=" OG SER G 328 " pdb=" OE1 GLN G 331 " model vdw 2.112 3.040 ... (remaining 176959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'B' selection = chain 'F' selection = chain 'H' } 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=0.00 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: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.540 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.004 0.114 22324 Z= 0.228 Angle : 0.676 9.253 30160 Z= 0.378 Chirality : 0.046 0.197 3448 Planarity : 0.013 0.304 3904 Dihedral : 15.364 89.692 8496 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.92 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.11 (0.15), residues: 2896 helix: 0.38 (0.15), residues: 1196 sheet: -1.09 (0.23), residues: 556 loop : -1.70 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 160 TYR 0.011 0.001 TYR D 167 PHE 0.036 0.003 PHE F 378 TRP 0.005 0.001 TRP D 294 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00396 (22320) covalent geometry : angle 0.67626 (30160) hydrogen bonds : bond 0.15852 ( 1104) hydrogen bonds : angle 6.19726 ( 3192) Misc. bond : bond 0.09793 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.626 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: D 157 VAL cc_start: 0.8906 (t) cc_final: 0.8688 (p) REVERT: B 157 VAL cc_start: 0.8877 (t) cc_final: 0.8662 (p) REVERT: B 178 GLN cc_start: 0.7783 (pp30) cc_final: 0.7566 (pp30) REVERT: F 157 VAL cc_start: 0.8873 (t) cc_final: 0.8660 (p) REVERT: H 157 VAL cc_start: 0.8851 (t) cc_final: 0.8626 (p) REVERT: H 269 LEU cc_start: 0.8643 (mt) cc_final: 0.8440 (mt) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.1456 time to fit residues: 97.2566 Evaluate side-chains 278 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0040 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN C 74 GLN A 74 GLN E 74 GLN G 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.129982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.100033 restraints weight = 83146.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.104230 restraints weight = 41995.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.107449 restraints weight = 26668.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.107960 restraints weight = 21566.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108329 restraints weight = 18706.721| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22324 Z= 0.159 Angle : 0.650 7.536 30160 Z= 0.341 Chirality : 0.048 0.207 3448 Planarity : 0.005 0.050 3904 Dihedral : 10.190 69.769 3288 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.75 % Favored : 95.11 % Rotamer: Outliers : 1.21 % Allowed : 10.49 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.99 (0.15), residues: 2896 helix: 0.63 (0.15), residues: 1176 sheet: -1.07 (0.23), residues: 552 loop : -1.74 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 165 TYR 0.016 0.001 TYR F 167 PHE 0.016 0.002 PHE D 111 TRP 0.003 0.001 TRP H 294 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00374 (22320) covalent geometry : angle 0.64981 (30160) hydrogen bonds : bond 0.04128 ( 1104) hydrogen bonds : angle 4.91596 ( 3192) Misc. bond : bond 0.00298 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 295 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 157 VAL cc_start: 0.9011 (t) cc_final: 0.8742 (p) REVERT: D 260 MET cc_start: 0.8498 (ttm) cc_final: 0.8201 (ttt) REVERT: D 329 MET cc_start: 0.8035 (mtm) cc_final: 0.7814 (mtm) REVERT: B 157 VAL cc_start: 0.8989 (t) cc_final: 0.8731 (p) REVERT: B 178 GLN cc_start: 0.8083 (pp30) cc_final: 0.7786 (pp30) REVERT: B 329 MET cc_start: 0.7999 (mtm) cc_final: 0.7773 (mtm) REVERT: F 157 VAL cc_start: 0.9004 (t) cc_final: 0.8741 (p) REVERT: F 254 MET cc_start: 0.7973 (tmm) cc_final: 0.7648 (tmm) REVERT: F 329 MET cc_start: 0.7950 (mtm) cc_final: 0.7730 (mtm) REVERT: H 157 VAL cc_start: 0.8969 (t) cc_final: 0.8711 (p) REVERT: H 254 MET cc_start: 0.7998 (tmm) cc_final: 0.7677 (tmm) REVERT: H 329 MET cc_start: 0.8005 (mtm) cc_final: 0.7774 (mtm) outliers start: 28 outliers final: 14 residues processed: 307 average time/residue: 0.1355 time to fit residues: 69.4358 Evaluate side-chains 280 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 266 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain F residue 454 HIS Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain H residue 454 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 229 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 GLN C 220 GLN D 239 ASN A 150 GLN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN E 150 GLN G 150 GLN ** G 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.124204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092442 restraints weight = 109962.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.096818 restraints weight = 69599.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.100312 restraints weight = 37531.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101294 restraints weight = 25622.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102090 restraints weight = 24144.494| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 22324 Z= 0.235 Angle : 0.655 9.409 30160 Z= 0.345 Chirality : 0.048 0.167 3448 Planarity : 0.005 0.049 3904 Dihedral : 9.980 71.057 3288 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.96 % Favored : 93.90 % Rotamer: Outliers : 1.99 % Allowed : 13.26 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.05 (0.15), residues: 2896 helix: 0.57 (0.15), residues: 1176 sheet: -1.24 (0.23), residues: 556 loop : -1.68 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.013 0.002 TYR F 167 PHE 0.024 0.002 PHE B 247 TRP 0.003 0.001 TRP H 294 HIS 0.004 0.001 HIS G 299 Details of bonding type rmsd covalent geometry : bond 0.00562 (22320) covalent geometry : angle 0.65514 (30160) hydrogen bonds : bond 0.03905 ( 1104) hydrogen bonds : angle 4.82877 ( 3192) Misc. bond : bond 0.00028 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 329 MET cc_start: 0.8155 (mtm) cc_final: 0.7938 (mtm) REVERT: B 178 GLN cc_start: 0.8236 (pp30) cc_final: 0.7940 (pp30) REVERT: B 329 MET cc_start: 0.8174 (mtm) cc_final: 0.7934 (mtm) REVERT: F 329 MET cc_start: 0.8123 (mtm) cc_final: 0.7912 (mtm) outliers start: 46 outliers final: 36 residues processed: 294 average time/residue: 0.1314 time to fit residues: 65.0428 Evaluate side-chains 280 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 345 PHE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 255 ILE Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 345 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 20 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 chunk 97 optimal weight: 0.0000 chunk 121 optimal weight: 4.9990 chunk 189 optimal weight: 0.4980 chunk 175 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.127690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095007 restraints weight = 106719.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100695 restraints weight = 55470.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.103800 restraints weight = 30384.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.104560 restraints weight = 22477.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105003 restraints weight = 22513.441| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22324 Z= 0.124 Angle : 0.579 11.277 30160 Z= 0.303 Chirality : 0.046 0.174 3448 Planarity : 0.004 0.047 3904 Dihedral : 9.845 72.341 3288 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.82 % Favored : 95.04 % Rotamer: Outliers : 1.90 % Allowed : 14.42 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.89 (0.15), residues: 2896 helix: 0.75 (0.15), residues: 1188 sheet: -1.19 (0.23), residues: 552 loop : -1.66 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 165 TYR 0.010 0.001 TYR E 207 PHE 0.013 0.002 PHE C 231 TRP 0.003 0.001 TRP H 294 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00297 (22320) covalent geometry : angle 0.57909 (30160) hydrogen bonds : bond 0.03424 ( 1104) hydrogen bonds : angle 4.57052 ( 3192) Misc. bond : bond 0.00022 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 329 MET cc_start: 0.8149 (mtm) cc_final: 0.7637 (mtm) REVERT: B 178 GLN cc_start: 0.8141 (pp30) cc_final: 0.7850 (pp30) REVERT: B 329 MET cc_start: 0.8145 (mtm) cc_final: 0.7606 (mtm) REVERT: F 329 MET cc_start: 0.8116 (mtm) cc_final: 0.7881 (mtm) REVERT: G 58 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7847 (pt) outliers start: 44 outliers final: 23 residues processed: 316 average time/residue: 0.1351 time to fit residues: 72.2274 Evaluate side-chains 288 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 345 PHE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 345 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 110 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 224 optimal weight: 0.0980 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN ** E 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.127013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.095895 restraints weight = 110355.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.100444 restraints weight = 71714.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.104005 restraints weight = 37171.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.105491 restraints weight = 25275.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106063 restraints weight = 22904.497| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22324 Z= 0.153 Angle : 0.587 13.003 30160 Z= 0.307 Chirality : 0.046 0.179 3448 Planarity : 0.004 0.046 3904 Dihedral : 9.796 73.043 3288 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.96 % Favored : 94.90 % Rotamer: Outliers : 2.29 % Allowed : 15.41 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.16), residues: 2896 helix: 0.73 (0.15), residues: 1180 sheet: -1.06 (0.23), residues: 548 loop : -1.68 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 165 TYR 0.009 0.001 TYR D 58 PHE 0.021 0.002 PHE D 361 TRP 0.003 0.001 TRP F 294 HIS 0.003 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00372 (22320) covalent geometry : angle 0.58708 (30160) hydrogen bonds : bond 0.03400 ( 1104) hydrogen bonds : angle 4.56655 ( 3192) Misc. bond : bond 0.00027 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 374 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7419 (pp) REVERT: A 58 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7901 (pt) REVERT: B 178 GLN cc_start: 0.8140 (pp30) cc_final: 0.7844 (pp30) REVERT: B 374 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7529 (pp) REVERT: E 58 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8005 (pt) REVERT: F 329 MET cc_start: 0.8091 (mtm) cc_final: 0.7840 (mtm) REVERT: F 374 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7626 (pp) REVERT: G 58 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7983 (pt) REVERT: H 374 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7506 (pp) outliers start: 53 outliers final: 36 residues processed: 300 average time/residue: 0.1336 time to fit residues: 67.8544 Evaluate side-chains 303 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 345 PHE Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 166 GLU Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 374 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 65 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.126088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095642 restraints weight = 94132.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.100114 restraints weight = 46093.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101905 restraints weight = 29770.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102754 restraints weight = 25955.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.102999 restraints weight = 22456.879| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22324 Z= 0.168 Angle : 0.597 13.715 30160 Z= 0.309 Chirality : 0.046 0.165 3448 Planarity : 0.004 0.046 3904 Dihedral : 9.855 74.132 3288 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.61 % Favored : 95.25 % Rotamer: Outliers : 2.81 % Allowed : 15.67 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.91 (0.16), residues: 2896 helix: 0.66 (0.15), residues: 1212 sheet: -1.11 (0.23), residues: 548 loop : -1.68 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 165 TYR 0.017 0.001 TYR D 75 PHE 0.017 0.002 PHE B 247 TRP 0.003 0.001 TRP F 294 HIS 0.005 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00401 (22320) covalent geometry : angle 0.59706 (30160) hydrogen bonds : bond 0.03393 ( 1104) hydrogen bonds : angle 4.49959 ( 3192) Misc. bond : bond 0.00032 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 265 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 374 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7657 (pp) REVERT: A 58 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7949 (pt) REVERT: B 178 GLN cc_start: 0.8169 (pp30) cc_final: 0.7864 (pp30) REVERT: B 374 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7290 (pp) REVERT: E 58 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8019 (mm) REVERT: F 329 MET cc_start: 0.8150 (mtm) cc_final: 0.7911 (mtm) REVERT: F 374 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7565 (pp) REVERT: G 58 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7933 (pt) REVERT: H 374 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7427 (pp) outliers start: 65 outliers final: 37 residues processed: 310 average time/residue: 0.1264 time to fit residues: 66.3899 Evaluate side-chains 293 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 162 GLN Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 345 PHE Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 374 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 109 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 174 optimal weight: 0.2980 chunk 260 optimal weight: 0.6980 chunk 262 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 257 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 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 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.128391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096325 restraints weight = 115134.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101284 restraints weight = 72252.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.106420 restraints weight = 37470.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106800 restraints weight = 23609.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107853 restraints weight = 22938.393| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 22324 Z= 0.121 Angle : 0.574 13.506 30160 Z= 0.295 Chirality : 0.045 0.168 3448 Planarity : 0.004 0.045 3904 Dihedral : 9.743 74.463 3288 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.40 % Favored : 95.46 % Rotamer: Outliers : 1.99 % Allowed : 16.54 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.74 (0.16), residues: 2896 helix: 0.82 (0.15), residues: 1196 sheet: -1.05 (0.24), residues: 508 loop : -1.57 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 165 TYR 0.022 0.001 TYR D 75 PHE 0.013 0.001 PHE E 231 TRP 0.003 0.001 TRP F 294 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00296 (22320) covalent geometry : angle 0.57393 (30160) hydrogen bonds : bond 0.03167 ( 1104) hydrogen bonds : angle 4.34891 ( 3192) Misc. bond : bond 0.00026 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 374 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7249 (pp) REVERT: A 58 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.8022 (mm) REVERT: B 178 GLN cc_start: 0.8045 (pp30) cc_final: 0.7774 (pp30) REVERT: B 374 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7241 (pp) REVERT: E 58 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8062 (mm) REVERT: F 329 MET cc_start: 0.8147 (mtm) cc_final: 0.7874 (mtm) REVERT: F 374 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7245 (pp) REVERT: G 58 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7995 (mm) REVERT: H 374 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7243 (pp) outliers start: 46 outliers final: 31 residues processed: 309 average time/residue: 0.1368 time to fit residues: 71.7627 Evaluate side-chains 291 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 345 PHE Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 374 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 153 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.0010 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 0.4980 chunk 193 optimal weight: 7.9990 chunk 191 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.127715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.096242 restraints weight = 111952.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101015 restraints weight = 69421.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.104711 restraints weight = 35623.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.106035 restraints weight = 24336.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.106632 restraints weight = 22207.443| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 22324 Z= 0.137 Angle : 0.588 13.325 30160 Z= 0.302 Chirality : 0.046 0.210 3448 Planarity : 0.004 0.045 3904 Dihedral : 9.734 74.587 3288 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.51 % Favored : 95.35 % Rotamer: Outliers : 1.94 % Allowed : 17.53 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.77 (0.16), residues: 2896 helix: 0.83 (0.15), residues: 1196 sheet: -1.05 (0.23), residues: 548 loop : -1.63 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 165 TYR 0.016 0.001 TYR D 75 PHE 0.023 0.001 PHE F 361 TRP 0.003 0.001 TRP F 294 HIS 0.006 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00335 (22320) covalent geometry : angle 0.58827 (30160) hydrogen bonds : bond 0.03167 ( 1104) hydrogen bonds : angle 4.33576 ( 3192) Misc. bond : bond 0.00026 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 374 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7530 (pp) REVERT: A 58 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8080 (mm) REVERT: A 164 LYS cc_start: 0.7993 (tppt) cc_final: 0.7740 (ptpp) REVERT: B 178 GLN cc_start: 0.8046 (pp30) cc_final: 0.7776 (pp30) REVERT: B 374 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7538 (pp) REVERT: E 58 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8079 (mm) REVERT: F 329 MET cc_start: 0.8146 (mtm) cc_final: 0.7888 (mtm) REVERT: F 374 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7422 (pp) REVERT: G 58 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8078 (mm) REVERT: H 374 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7344 (pp) outliers start: 45 outliers final: 30 residues processed: 291 average time/residue: 0.1325 time to fit residues: 65.6557 Evaluate side-chains 287 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 345 PHE Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 375 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 124 optimal weight: 8.9990 chunk 280 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 319 GLN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN F 239 ASN G 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.126400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095089 restraints weight = 117259.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.100273 restraints weight = 71237.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.103841 restraints weight = 35778.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.105066 restraints weight = 24407.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.105719 restraints weight = 22153.726| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 22324 Z= 0.168 Angle : 0.609 13.655 30160 Z= 0.312 Chirality : 0.046 0.175 3448 Planarity : 0.004 0.045 3904 Dihedral : 9.850 75.484 3288 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.85 % Favored : 95.01 % Rotamer: Outliers : 2.25 % Allowed : 17.83 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.80 (0.16), residues: 2896 helix: 0.78 (0.15), residues: 1196 sheet: -1.09 (0.23), residues: 548 loop : -1.61 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.013 0.001 TYR H 75 PHE 0.024 0.002 PHE F 361 TRP 0.002 0.001 TRP F 294 HIS 0.003 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00411 (22320) covalent geometry : angle 0.60879 (30160) hydrogen bonds : bond 0.03287 ( 1104) hydrogen bonds : angle 4.38190 ( 3192) Misc. bond : bond 0.00030 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 374 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7556 (pp) REVERT: A 58 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8109 (mm) REVERT: A 164 LYS cc_start: 0.8048 (tppt) cc_final: 0.7829 (ptpp) REVERT: B 178 GLN cc_start: 0.8053 (pp30) cc_final: 0.7788 (pp30) REVERT: B 374 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7546 (pp) REVERT: E 58 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8177 (mm) REVERT: F 178 GLN cc_start: 0.8111 (pp30) cc_final: 0.7878 (pp30) REVERT: F 329 MET cc_start: 0.8186 (mtm) cc_final: 0.7900 (mtm) REVERT: F 374 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7389 (pp) REVERT: G 58 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8172 (mm) REVERT: H 374 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7322 (pp) outliers start: 52 outliers final: 33 residues processed: 294 average time/residue: 0.1217 time to fit residues: 60.5222 Evaluate side-chains 290 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 345 PHE Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 173 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 184 optimal weight: 20.0000 chunk 217 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN B 239 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN E 220 GLN G 220 GLN H 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.090516 restraints weight = 103473.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094760 restraints weight = 68997.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.097746 restraints weight = 36042.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098480 restraints weight = 25622.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.099094 restraints weight = 24100.297| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 22324 Z= 0.322 Angle : 0.758 14.180 30160 Z= 0.391 Chirality : 0.051 0.241 3448 Planarity : 0.005 0.048 3904 Dihedral : 10.527 77.728 3288 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.55 % Favored : 93.31 % Rotamer: Outliers : 2.16 % Allowed : 17.83 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.23 (0.16), residues: 2896 helix: 0.38 (0.15), residues: 1180 sheet: -1.43 (0.23), residues: 556 loop : -1.68 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 166 TYR 0.018 0.002 TYR F 75 PHE 0.032 0.003 PHE B 247 TRP 0.001 0.001 TRP D 294 HIS 0.005 0.002 HIS G 299 Details of bonding type rmsd covalent geometry : bond 0.00767 (22320) covalent geometry : angle 0.75779 (30160) hydrogen bonds : bond 0.03991 ( 1104) hydrogen bonds : angle 4.83561 ( 3192) Misc. bond : bond 0.00049 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: C 60 CYS cc_start: 0.8036 (t) cc_final: 0.7795 (t) REVERT: D 374 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8114 (pp) REVERT: A 58 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8207 (mm) REVERT: A 164 LYS cc_start: 0.8137 (tppt) cc_final: 0.7823 (ptpp) REVERT: B 178 GLN cc_start: 0.8316 (pp30) cc_final: 0.8010 (pp30) REVERT: B 374 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8114 (pp) REVERT: E 58 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8093 (mm) REVERT: F 178 GLN cc_start: 0.8325 (pp30) cc_final: 0.8098 (pp30) REVERT: F 329 MET cc_start: 0.8203 (mtm) cc_final: 0.7975 (mtm) REVERT: F 374 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.7986 (pp) REVERT: G 58 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8091 (mm) REVERT: G 164 LYS cc_start: 0.8123 (tppt) cc_final: 0.7670 (pttm) REVERT: H 374 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.7959 (pp) outliers start: 50 outliers final: 30 residues processed: 265 average time/residue: 0.1280 time to fit residues: 57.8606 Evaluate side-chains 253 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 162 GLN Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 345 PHE Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 142 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 176 optimal weight: 0.0980 chunk 164 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN E 130 ASN E 220 GLN G 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.125699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093967 restraints weight = 86946.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.098939 restraints weight = 46101.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.102156 restraints weight = 28728.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103213 restraints weight = 22295.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.104226 restraints weight = 19241.564| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22324 Z= 0.134 Angle : 0.627 13.628 30160 Z= 0.322 Chirality : 0.047 0.178 3448 Planarity : 0.004 0.046 3904 Dihedral : 10.211 78.411 3288 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 1.25 % Allowed : 18.44 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2896 helix: 0.58 (0.15), residues: 1224 sheet: -1.28 (0.24), residues: 512 loop : -1.48 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 165 TYR 0.014 0.001 TYR H 75 PHE 0.020 0.002 PHE F 361 TRP 0.002 0.000 TRP H 294 HIS 0.006 0.001 HIS G 71 Details of bonding type rmsd covalent geometry : bond 0.00326 (22320) covalent geometry : angle 0.62655 (30160) hydrogen bonds : bond 0.03339 ( 1104) hydrogen bonds : angle 4.43901 ( 3192) Misc. bond : bond 0.00020 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3895.91 seconds wall clock time: 68 minutes 16.75 seconds (4096.75 seconds total)