Starting phenix.real_space_refine on Thu Sep 18 12:10:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c21_45135/09_2025/9c21_45135_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c21_45135/09_2025/9c21_45135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c21_45135/09_2025/9c21_45135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c21_45135/09_2025/9c21_45135.map" model { file = "/net/cci-nas-00/data/ceres_data/9c21_45135/09_2025/9c21_45135_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c21_45135/09_2025/9c21_45135_neut.cif" } resolution = 3.4 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 10656 2.51 5 N 2886 2.21 5 O 3036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16704 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2774 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 1, 'GLU:plan': 12, 'HIC:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 82 Conformer: "B" Number of residues, atoms: 371, 2774 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 1, 'GLU:plan': 12, 'HIC:plan-1': 1, 'HIC:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 91 bond proxies already assigned to first conformer: 2823 Restraints were copied for chains: B, C, D, E, F Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N BHIS A 73 " occ=0.50 ... (8 atoms not shown) pdb=" NE2BHIS A 73 " occ=0.50 residue: pdb=" N BHIS B 73 " occ=0.50 ... (8 atoms not shown) pdb=" NE2BHIS B 73 " occ=0.50 residue: pdb=" N BHIS C 73 " occ=0.50 ... (8 atoms not shown) pdb=" NE2BHIS C 73 " occ=0.50 residue: pdb=" N BHIS D 73 " occ=0.50 ... (8 atoms not shown) pdb=" NE2BHIS D 73 " occ=0.50 residue: pdb=" N BHIS E 73 " occ=0.50 ... (8 atoms not shown) pdb=" NE2BHIS E 73 " occ=0.50 residue: pdb=" N BHIS F 73 " occ=0.50 ... (8 atoms not shown) pdb=" NE2BHIS F 73 " occ=0.50 Time building chain proxies: 3.31, per 1000 atoms: 0.20 Number of scatterers: 16704 At special positions: 0 Unit cell: (91.67, 95.79, 218.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 3036 8.00 N 2886 7.00 C 10656 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=0, symmetry=0 Links applied TRANS "BHIS A 73 " - " GLU A 72 " : altloc "B" - "" "BHIS B 73 " - " GLU B 72 " : altloc "B" - "" "BHIS C 73 " - " GLU C 72 " : altloc "B" - "" "BHIS D 73 " - " GLU D 72 " : altloc "B" - "" "BHIS E 73 " - " GLU E 72 " : altloc "B" - "" "BHIS F 73 " - " GLU F 72 " : altloc "B" - "" Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 36 sheets defined 48.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.682A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.531A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.800A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.512A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.653A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.556A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 366 through 372 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.682A pdb=" N GLU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.531A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.801A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.513A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.653A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.556A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.683A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.530A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.800A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.512A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.653A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.557A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 366 through 372 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.682A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.531A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.800A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.513A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.653A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.556A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 366 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.682A pdb=" N GLU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.531A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.801A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 262 removed outlier: 3.513A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 285 removed outlier: 3.652A pdb=" N CYS E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.557A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 366 through 372 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 93 removed outlier: 3.681A pdb=" N GLU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.531A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.800A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 197 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 removed outlier: 3.512A pdb=" N LEU F 261 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 285 removed outlier: 3.652A pdb=" N CYS F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.557A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 366 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.273A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.581A pdb=" N VAL A 35 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.221A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 165 through 166 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.273A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.581A pdb=" N VAL B 35 " --> pdb=" O LYS B 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.222A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.273A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.581A pdb=" N VAL C 35 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.221A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 165 through 166 Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.274A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.581A pdb=" N VAL D 35 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.222A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.273A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.580A pdb=" N VAL E 35 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 176 through 178 removed outlier: 6.221A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 165 through 166 Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.274A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.582A pdb=" N VAL F 35 " --> pdb=" O LYS F 68 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 176 through 178 removed outlier: 6.222A pdb=" N THR F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 165 through 166 Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 846 hydrogen bonds defined for protein. 2322 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3391 1.33 - 1.45: 3890 1.45 - 1.57: 9585 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 17082 Sorted by residual: bond pdb=" CG BHIS E 73 " pdb=" ND1BHIS E 73 " ideal model delta sigma weight residual 1.378 1.312 0.066 1.10e-02 8.26e+03 3.59e+01 bond pdb=" CG BHIS D 73 " pdb=" ND1BHIS D 73 " ideal model delta sigma weight residual 1.378 1.312 0.066 1.10e-02 8.26e+03 3.55e+01 bond pdb=" CG BHIS F 73 " pdb=" ND1BHIS F 73 " ideal model delta sigma weight residual 1.378 1.312 0.066 1.10e-02 8.26e+03 3.55e+01 bond pdb=" CG BHIS C 73 " pdb=" ND1BHIS C 73 " ideal model delta sigma weight residual 1.378 1.313 0.065 1.10e-02 8.26e+03 3.50e+01 bond pdb=" CG BHIS A 73 " pdb=" ND1BHIS A 73 " ideal model delta sigma weight residual 1.378 1.313 0.065 1.10e-02 8.26e+03 3.47e+01 ... (remaining 17077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 22707 2.12 - 4.24: 460 4.24 - 6.36: 29 6.36 - 8.48: 12 8.48 - 10.60: 18 Bond angle restraints: 23226 Sorted by residual: angle pdb=" CA BHIS E 73 " pdb=" CB BHIS E 73 " pdb=" CG BHIS E 73 " ideal model delta sigma weight residual 113.80 108.89 4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" CA BHIS C 73 " pdb=" CB BHIS C 73 " pdb=" CG BHIS C 73 " ideal model delta sigma weight residual 113.80 108.93 4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" CA BHIS A 73 " pdb=" CB BHIS A 73 " pdb=" CG BHIS A 73 " ideal model delta sigma weight residual 113.80 108.95 4.85 1.00e+00 1.00e+00 2.36e+01 angle pdb=" CA BHIS D 73 " pdb=" CB BHIS D 73 " pdb=" CG BHIS D 73 " ideal model delta sigma weight residual 113.80 108.95 4.85 1.00e+00 1.00e+00 2.35e+01 angle pdb=" CA BHIS F 73 " pdb=" CB BHIS F 73 " pdb=" CG BHIS F 73 " ideal model delta sigma weight residual 113.80 108.95 4.85 1.00e+00 1.00e+00 2.35e+01 ... (remaining 23221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9120 17.97 - 35.94: 831 35.94 - 53.91: 231 53.91 - 71.88: 18 71.88 - 89.85: 18 Dihedral angle restraints: 10218 sinusoidal: 3786 harmonic: 6432 Sorted by residual: dihedral pdb=" C MET D 305 " pdb=" N MET D 305 " pdb=" CA MET D 305 " pdb=" CB MET D 305 " ideal model delta harmonic sigma weight residual -122.60 -136.34 13.74 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" C MET B 305 " pdb=" N MET B 305 " pdb=" CA MET B 305 " pdb=" CB MET B 305 " ideal model delta harmonic sigma weight residual -122.60 -136.32 13.72 0 2.50e+00 1.60e-01 3.01e+01 dihedral pdb=" C MET C 305 " pdb=" N MET C 305 " pdb=" CA MET C 305 " pdb=" CB MET C 305 " ideal model delta harmonic sigma weight residual -122.60 -136.31 13.71 0 2.50e+00 1.60e-01 3.01e+01 ... (remaining 10215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2505 0.091 - 0.182: 147 0.182 - 0.272: 6 0.272 - 0.363: 0 0.363 - 0.454: 6 Chirality restraints: 2664 Sorted by residual: chirality pdb=" CA MET D 305 " pdb=" N MET D 305 " pdb=" C MET D 305 " pdb=" CB MET D 305 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA MET B 305 " pdb=" N MET B 305 " pdb=" C MET B 305 " pdb=" CB MET B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA MET A 305 " pdb=" N MET A 305 " pdb=" C MET A 305 " pdb=" CB MET A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 ... (remaining 2661 not shown) Planarity restraints: 2964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 368 " 0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C SER C 368 " -0.085 2.00e-02 2.50e+03 pdb=" O SER C 368 " 0.032 2.00e-02 2.50e+03 pdb=" N ILE C 369 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 368 " 0.025 2.00e-02 2.50e+03 4.91e-02 2.42e+01 pdb=" C SER D 368 " -0.085 2.00e-02 2.50e+03 pdb=" O SER D 368 " 0.032 2.00e-02 2.50e+03 pdb=" N ILE D 369 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 368 " 0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C SER F 368 " -0.085 2.00e-02 2.50e+03 pdb=" O SER F 368 " 0.032 2.00e-02 2.50e+03 pdb=" N ILE F 369 " 0.028 2.00e-02 2.50e+03 ... (remaining 2961 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1020 2.73 - 3.27: 16970 3.27 - 3.81: 28761 3.81 - 4.36: 32259 4.36 - 4.90: 57017 Nonbonded interactions: 136027 Sorted by model distance: nonbonded pdb=" O GLY D 168 " pdb=" NE2 GLN E 49 " model vdw 2.183 3.120 nonbonded pdb=" OD2 ASP D 288 " pdb=" NE ARG E 62 " model vdw 2.185 3.120 nonbonded pdb=" OD2 ASP B 288 " pdb=" NE ARG C 62 " model vdw 2.196 3.120 nonbonded pdb=" OD2 ASP E 288 " pdb=" NE ARG F 62 " model vdw 2.197 3.120 nonbonded pdb=" O GLY B 168 " pdb=" NE2 GLN C 49 " model vdw 2.205 3.120 ... (remaining 136022 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.005 0.066 17088 Z= 0.286 Angle : 0.714 10.600 23244 Z= 0.398 Chirality : 0.049 0.454 2664 Planarity : 0.006 0.099 2958 Dihedral : 15.188 89.853 6084 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.42 % Allowed : 18.74 % Favored : 79.85 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.19), residues: 2208 helix: 1.27 (0.18), residues: 948 sheet: 0.92 (0.26), residues: 366 loop : -0.37 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 177 TYR 0.009 0.001 TYR D 362 PHE 0.009 0.001 PHE B 279 TRP 0.014 0.002 TRP A 356 HIS 0.002 0.000 BHIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00462 (17082) covalent geometry : angle 0.71370 (23226) hydrogen bonds : bond 0.14795 ( 846) hydrogen bonds : angle 6.24474 ( 2322) link_TRANS : bond 0.00432 ( 6) link_TRANS : angle 1.24400 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 0.614 Fit side-chains REVERT: A 370 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7216 (p) REVERT: B 59 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8202 (mm-40) REVERT: B 119 MET cc_start: 0.8356 (ttm) cc_final: 0.8123 (ttm) REVERT: C 16 MET cc_start: 0.7897 (mtp) cc_final: 0.7613 (mtp) REVERT: C 94 LEU cc_start: 0.9133 (mp) cc_final: 0.8832 (mt) REVERT: C 153 MET cc_start: 0.8590 (tmm) cc_final: 0.8308 (tmm) REVERT: D 227 MET cc_start: 0.8788 (mmm) cc_final: 0.8212 (tpp) REVERT: D 313 MET cc_start: 0.8697 (ttm) cc_final: 0.8115 (ttt) REVERT: E 81 ASP cc_start: 0.8043 (m-30) cc_final: 0.7805 (m-30) REVERT: F 44 MET cc_start: 0.8370 (mmm) cc_final: 0.7934 (mmp) REVERT: F 159 VAL cc_start: 0.8841 (t) cc_final: 0.8573 (m) REVERT: F 227 MET cc_start: 0.8762 (mmm) cc_final: 0.8464 (tpp) outliers start: 24 outliers final: 14 residues processed: 298 average time/residue: 0.1023 time to fit residues: 50.7789 Evaluate side-chains 236 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 221 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 369 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.0370 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS D 225 GLN E 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087847 restraints weight = 106351.688| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 5.85 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17088 Z= 0.196 Angle : 0.595 7.735 23244 Z= 0.315 Chirality : 0.046 0.155 2664 Planarity : 0.006 0.087 2958 Dihedral : 5.141 46.339 2445 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.01 % Allowed : 17.73 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.18), residues: 2208 helix: 1.32 (0.18), residues: 966 sheet: 0.86 (0.27), residues: 366 loop : -0.34 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.018 0.001 TYR C 306 PHE 0.035 0.002 PHE F 279 TRP 0.013 0.002 TRP A 356 HIS 0.008 0.001 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00462 (17082) covalent geometry : angle 0.59513 (23226) hydrogen bonds : bond 0.03737 ( 846) hydrogen bonds : angle 5.06885 ( 2322) link_TRANS : bond 0.00022 ( 6) link_TRANS : angle 0.33020 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 220 time to evaluate : 0.550 Fit side-chains REVERT: B 119 MET cc_start: 0.8409 (ttm) cc_final: 0.8201 (ttm) REVERT: C 94 LEU cc_start: 0.9233 (mp) cc_final: 0.8865 (mt) REVERT: D 82 MET cc_start: 0.8028 (tpp) cc_final: 0.7742 (ttp) REVERT: D 222 ASP cc_start: 0.7613 (p0) cc_final: 0.6917 (p0) REVERT: D 227 MET cc_start: 0.8288 (mmm) cc_final: 0.7526 (tpp) REVERT: D 313 MET cc_start: 0.8693 (ttm) cc_final: 0.8153 (ttt) REVERT: E 78 ASN cc_start: 0.7682 (t0) cc_final: 0.7073 (t0) REVERT: F 227 MET cc_start: 0.8305 (mmm) cc_final: 0.7733 (tpp) REVERT: F 279 PHE cc_start: 0.6672 (t80) cc_final: 0.6466 (t80) outliers start: 51 outliers final: 37 residues processed: 259 average time/residue: 0.0951 time to fit residues: 41.5790 Evaluate side-chains 232 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 369 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 172 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 189 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.094128 restraints weight = 92247.610| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 5.11 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17088 Z= 0.134 Angle : 0.540 10.184 23244 Z= 0.282 Chirality : 0.044 0.135 2664 Planarity : 0.005 0.074 2958 Dihedral : 4.528 44.574 2438 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.31 % Allowed : 18.09 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.18), residues: 2208 helix: 1.43 (0.18), residues: 966 sheet: 1.07 (0.27), residues: 366 loop : -0.21 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 147 TYR 0.018 0.001 TYR A 143 PHE 0.018 0.001 PHE B 352 TRP 0.024 0.002 TRP B 356 HIS 0.004 0.000 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00317 (17082) covalent geometry : angle 0.54027 (23226) hydrogen bonds : bond 0.03205 ( 846) hydrogen bonds : angle 4.80244 ( 2322) link_TRANS : bond 0.00090 ( 6) link_TRANS : angle 0.50571 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 0.543 Fit side-chains REVERT: A 117 GLU cc_start: 0.6768 (tp30) cc_final: 0.6400 (tp30) REVERT: A 222 ASP cc_start: 0.7282 (p0) cc_final: 0.6581 (p0) REVERT: C 94 LEU cc_start: 0.9217 (mp) cc_final: 0.8861 (mt) REVERT: D 82 MET cc_start: 0.8173 (tpp) cc_final: 0.7766 (tpp) REVERT: D 227 MET cc_start: 0.8454 (mmm) cc_final: 0.7641 (tpp) REVERT: D 241 GLU cc_start: 0.7681 (tp30) cc_final: 0.7444 (tt0) REVERT: E 159 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8273 (m) REVERT: F 227 MET cc_start: 0.8437 (mmm) cc_final: 0.7871 (tpp) REVERT: F 279 PHE cc_start: 0.6875 (t80) cc_final: 0.6612 (t80) outliers start: 56 outliers final: 43 residues processed: 255 average time/residue: 0.0891 time to fit residues: 38.9817 Evaluate side-chains 249 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 369 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 104 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 38 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092602 restraints weight = 103798.269| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 5.50 r_work: 0.3130 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17088 Z= 0.132 Angle : 0.528 11.227 23244 Z= 0.276 Chirality : 0.044 0.136 2664 Planarity : 0.005 0.067 2958 Dihedral : 4.381 45.372 2436 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.72 % Allowed : 17.85 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.18), residues: 2208 helix: 1.49 (0.17), residues: 966 sheet: 1.11 (0.27), residues: 372 loop : -0.13 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 147 TYR 0.016 0.001 TYR D 143 PHE 0.013 0.001 PHE F 279 TRP 0.024 0.002 TRP B 356 HIS 0.003 0.000 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00309 (17082) covalent geometry : angle 0.52836 (23226) hydrogen bonds : bond 0.03066 ( 846) hydrogen bonds : angle 4.69433 ( 2322) link_TRANS : bond 0.00102 ( 6) link_TRANS : angle 0.55148 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 0.652 Fit side-chains REVERT: A 222 ASP cc_start: 0.7338 (p0) cc_final: 0.6696 (p0) REVERT: C 94 LEU cc_start: 0.9246 (mp) cc_final: 0.8935 (mt) REVERT: C 207 GLU cc_start: 0.8112 (tp30) cc_final: 0.7703 (tp30) REVERT: D 222 ASP cc_start: 0.7538 (p0) cc_final: 0.6954 (p0) REVERT: D 227 MET cc_start: 0.8544 (mmm) cc_final: 0.7693 (tpp) REVERT: E 44 MET cc_start: 0.8863 (mmm) cc_final: 0.8414 (mmp) REVERT: E 159 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8459 (m) REVERT: F 227 MET cc_start: 0.8421 (mmm) cc_final: 0.7889 (tpp) REVERT: F 279 PHE cc_start: 0.7071 (t80) cc_final: 0.6781 (t80) outliers start: 63 outliers final: 59 residues processed: 263 average time/residue: 0.0971 time to fit residues: 43.8175 Evaluate side-chains 255 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 195 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 369 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 215 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 198 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.100160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.083901 restraints weight = 128346.103| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 5.71 r_work: 0.2992 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17088 Z= 0.251 Angle : 0.619 12.263 23244 Z= 0.328 Chirality : 0.048 0.143 2664 Planarity : 0.005 0.070 2958 Dihedral : 5.112 48.053 2436 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.26 % Allowed : 17.55 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.18), residues: 2208 helix: 1.29 (0.17), residues: 966 sheet: 1.00 (0.28), residues: 372 loop : -0.34 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 116 TYR 0.020 0.002 TYR A 143 PHE 0.015 0.002 PHE C 200 TRP 0.020 0.003 TRP B 356 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00592 (17082) covalent geometry : angle 0.61868 (23226) hydrogen bonds : bond 0.03765 ( 846) hydrogen bonds : angle 5.00900 ( 2322) link_TRANS : bond 0.00052 ( 6) link_TRANS : angle 0.69440 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 202 time to evaluate : 0.472 Fit side-chains REVERT: A 153 MET cc_start: 0.8240 (tmm) cc_final: 0.7953 (tmm) REVERT: B 78 ASN cc_start: 0.8225 (t0) cc_final: 0.7400 (t0) REVERT: B 153 MET cc_start: 0.8673 (tmm) cc_final: 0.8465 (tmm) REVERT: C 132 MET cc_start: 0.8614 (tmm) cc_final: 0.8296 (tmm) REVERT: D 169 TYR cc_start: 0.8328 (m-10) cc_final: 0.8042 (m-10) REVERT: E 44 MET cc_start: 0.8971 (mmm) cc_final: 0.8508 (mmp) REVERT: E 78 ASN cc_start: 0.8205 (t0) cc_final: 0.7484 (t0) REVERT: E 143 TYR cc_start: 0.8140 (m-80) cc_final: 0.7889 (m-80) REVERT: E 159 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8226 (m) REVERT: F 227 MET cc_start: 0.8250 (mmm) cc_final: 0.7737 (tpp) REVERT: F 279 PHE cc_start: 0.6960 (t80) cc_final: 0.6515 (t80) outliers start: 72 outliers final: 61 residues processed: 260 average time/residue: 0.0978 time to fit residues: 43.2475 Evaluate side-chains 253 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 191 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 369 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 5 optimal weight: 6.9990 chunk 110 optimal weight: 0.0570 chunk 178 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN D 225 GLN F 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.102918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.085110 restraints weight = 112902.807| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 6.00 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17088 Z= 0.143 Angle : 0.541 13.708 23244 Z= 0.284 Chirality : 0.044 0.136 2664 Planarity : 0.005 0.064 2958 Dihedral : 4.695 49.151 2436 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.84 % Allowed : 18.38 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.18), residues: 2208 helix: 1.37 (0.17), residues: 966 sheet: 1.04 (0.28), residues: 372 loop : -0.23 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 116 TYR 0.016 0.001 TYR B 143 PHE 0.010 0.001 PHE F 279 TRP 0.022 0.002 TRP B 356 HIS 0.003 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00335 (17082) covalent geometry : angle 0.54047 (23226) hydrogen bonds : bond 0.03151 ( 846) hydrogen bonds : angle 4.71504 ( 2322) link_TRANS : bond 0.00093 ( 6) link_TRANS : angle 0.58400 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 205 time to evaluate : 0.642 Fit side-chains REVERT: A 153 MET cc_start: 0.7651 (tmm) cc_final: 0.7326 (tmm) REVERT: B 269 MET cc_start: 0.8568 (mtm) cc_final: 0.8331 (ptp) REVERT: C 132 MET cc_start: 0.8494 (tmm) cc_final: 0.8206 (tmm) REVERT: C 207 GLU cc_start: 0.7949 (tp30) cc_final: 0.7558 (tp30) REVERT: D 227 MET cc_start: 0.8242 (mmm) cc_final: 0.7374 (tpp) REVERT: E 44 MET cc_start: 0.8954 (mmm) cc_final: 0.8367 (mmp) REVERT: E 143 TYR cc_start: 0.8029 (m-80) cc_final: 0.7765 (m-80) REVERT: E 159 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8078 (m) REVERT: F 227 MET cc_start: 0.8107 (mmm) cc_final: 0.7501 (tpp) REVERT: F 279 PHE cc_start: 0.6763 (t80) cc_final: 0.6469 (t80) outliers start: 65 outliers final: 60 residues processed: 263 average time/residue: 0.0957 time to fit residues: 42.8101 Evaluate side-chains 254 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 369 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 163 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 101 HIS ** 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 = 0.3383 r_free = 0.3383 target = 0.103414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.085538 restraints weight = 109886.555| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 6.09 r_work: 0.2897 rms_B_bonded: 6.09 restraints_weight: 2.0000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17088 Z= 0.128 Angle : 0.536 14.241 23244 Z= 0.280 Chirality : 0.044 0.137 2664 Planarity : 0.005 0.062 2958 Dihedral : 4.414 49.065 2434 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.90 % Allowed : 18.97 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.18), residues: 2208 helix: 1.45 (0.17), residues: 966 sheet: 1.05 (0.28), residues: 372 loop : -0.14 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 147 TYR 0.012 0.001 TYR F 198 PHE 0.022 0.001 PHE D 352 TRP 0.038 0.002 TRP D 356 HIS 0.005 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00299 (17082) covalent geometry : angle 0.53574 (23226) hydrogen bonds : bond 0.03057 ( 846) hydrogen bonds : angle 4.61146 ( 2322) link_TRANS : bond 0.00126 ( 6) link_TRANS : angle 0.63034 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 206 time to evaluate : 0.685 Fit side-chains REVERT: A 153 MET cc_start: 0.8104 (tmm) cc_final: 0.7776 (tmm) REVERT: C 132 MET cc_start: 0.8551 (tmm) cc_final: 0.8271 (tmm) REVERT: D 169 TYR cc_start: 0.8164 (m-10) cc_final: 0.7900 (m-10) REVERT: D 227 MET cc_start: 0.8329 (mmm) cc_final: 0.7507 (tpp) REVERT: E 44 MET cc_start: 0.9097 (mmm) cc_final: 0.8437 (mmp) REVERT: E 143 TYR cc_start: 0.8100 (m-80) cc_final: 0.7852 (m-80) REVERT: E 159 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8271 (m) REVERT: F 227 MET cc_start: 0.8232 (mmm) cc_final: 0.7602 (tpp) REVERT: F 279 PHE cc_start: 0.6917 (t80) cc_final: 0.6609 (t80) outliers start: 66 outliers final: 60 residues processed: 261 average time/residue: 0.1024 time to fit residues: 45.7467 Evaluate side-chains 259 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 198 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 369 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 211 optimal weight: 0.0000 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 22 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.084253 restraints weight = 110537.911| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 6.04 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17088 Z= 0.103 Angle : 0.513 14.140 23244 Z= 0.267 Chirality : 0.043 0.136 2664 Planarity : 0.005 0.058 2958 Dihedral : 4.151 49.458 2432 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.72 % Allowed : 19.33 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.18), residues: 2208 helix: 1.55 (0.17), residues: 966 sheet: 1.13 (0.28), residues: 372 loop : -0.03 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 147 TYR 0.015 0.001 TYR B 143 PHE 0.013 0.001 PHE D 352 TRP 0.029 0.002 TRP B 356 HIS 0.006 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00239 (17082) covalent geometry : angle 0.51301 (23226) hydrogen bonds : bond 0.02824 ( 846) hydrogen bonds : angle 4.49145 ( 2322) link_TRANS : bond 0.00167 ( 6) link_TRANS : angle 0.62299 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 228 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8456 (t) cc_final: 0.8090 (t) REVERT: A 153 MET cc_start: 0.7587 (tmm) cc_final: 0.7246 (tmm) REVERT: C 132 MET cc_start: 0.8483 (tmm) cc_final: 0.8237 (tmm) REVERT: C 143 TYR cc_start: 0.6864 (m-80) cc_final: 0.6434 (m-10) REVERT: C 207 GLU cc_start: 0.7822 (tp30) cc_final: 0.7513 (tp30) REVERT: E 44 MET cc_start: 0.8955 (mmm) cc_final: 0.8543 (mmp) REVERT: E 159 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8189 (m) REVERT: F 227 MET cc_start: 0.8159 (mmm) cc_final: 0.7578 (tpp) REVERT: F 279 PHE cc_start: 0.6698 (t80) cc_final: 0.6493 (t80) outliers start: 63 outliers final: 55 residues processed: 278 average time/residue: 0.1036 time to fit residues: 48.8389 Evaluate side-chains 273 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 217 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 369 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 140 optimal weight: 0.9990 chunk 32 optimal weight: 0.0070 chunk 180 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 160 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN F 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.085199 restraints weight = 102237.398| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 5.78 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17088 Z= 0.099 Angle : 0.512 14.334 23244 Z= 0.265 Chirality : 0.043 0.141 2664 Planarity : 0.005 0.056 2958 Dihedral : 4.107 49.983 2432 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.37 % Allowed : 20.27 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2208 helix: 1.62 (0.17), residues: 966 sheet: 1.25 (0.28), residues: 372 loop : 0.00 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 147 TYR 0.014 0.001 TYR F 198 PHE 0.009 0.001 PHE F 279 TRP 0.032 0.002 TRP B 356 HIS 0.008 0.000 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00228 (17082) covalent geometry : angle 0.51220 (23226) hydrogen bonds : bond 0.02788 ( 846) hydrogen bonds : angle 4.46554 ( 2322) link_TRANS : bond 0.00170 ( 6) link_TRANS : angle 0.66854 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 221 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8448 (t) cc_final: 0.8045 (t) REVERT: A 117 GLU cc_start: 0.6593 (tp30) cc_final: 0.6243 (tp30) REVERT: A 153 MET cc_start: 0.7539 (tmm) cc_final: 0.7190 (tmm) REVERT: A 283 MET cc_start: 0.8358 (mmm) cc_final: 0.8105 (mmm) REVERT: B 119 MET cc_start: 0.8491 (ttm) cc_final: 0.8277 (ttm) REVERT: C 132 MET cc_start: 0.8475 (tmm) cc_final: 0.8224 (tmm) REVERT: C 143 TYR cc_start: 0.6787 (m-80) cc_final: 0.6322 (m-10) REVERT: C 207 GLU cc_start: 0.7828 (tp30) cc_final: 0.7503 (tp30) REVERT: E 44 MET cc_start: 0.8981 (mmm) cc_final: 0.8558 (mmp) REVERT: E 159 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8218 (m) REVERT: F 227 MET cc_start: 0.8173 (mmm) cc_final: 0.7609 (tpp) REVERT: F 279 PHE cc_start: 0.6772 (t80) cc_final: 0.6531 (t80) outliers start: 57 outliers final: 56 residues processed: 266 average time/residue: 0.1034 time to fit residues: 46.5881 Evaluate side-chains 270 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 369 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 182 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 70 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 88 optimal weight: 0.0270 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.106603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.089224 restraints weight = 90841.203| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 5.51 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17088 Z= 0.111 Angle : 0.518 14.587 23244 Z= 0.269 Chirality : 0.043 0.185 2664 Planarity : 0.005 0.056 2958 Dihedral : 4.119 49.954 2432 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.37 % Allowed : 19.92 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.18), residues: 2208 helix: 1.65 (0.17), residues: 966 sheet: 1.25 (0.28), residues: 372 loop : -0.01 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 147 TYR 0.015 0.001 TYR F 198 PHE 0.009 0.001 PHE F 279 TRP 0.032 0.002 TRP B 356 HIS 0.007 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00259 (17082) covalent geometry : angle 0.51815 (23226) hydrogen bonds : bond 0.02906 ( 846) hydrogen bonds : angle 4.45802 ( 2322) link_TRANS : bond 0.00138 ( 6) link_TRANS : angle 0.68265 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 217 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8467 (t) cc_final: 0.8068 (t) REVERT: A 153 MET cc_start: 0.7517 (tmm) cc_final: 0.7158 (tmm) REVERT: A 283 MET cc_start: 0.8363 (mmm) cc_final: 0.8113 (mmm) REVERT: C 132 MET cc_start: 0.8450 (tmm) cc_final: 0.8206 (tmm) REVERT: C 143 TYR cc_start: 0.6790 (m-80) cc_final: 0.6319 (m-10) REVERT: C 207 GLU cc_start: 0.7838 (tp30) cc_final: 0.7482 (tp30) REVERT: E 44 MET cc_start: 0.9006 (mmm) cc_final: 0.8585 (mmp) REVERT: E 159 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8179 (m) REVERT: F 227 MET cc_start: 0.8176 (mmm) cc_final: 0.7610 (tpp) outliers start: 57 outliers final: 56 residues processed: 262 average time/residue: 0.1087 time to fit residues: 48.0320 Evaluate side-chains 269 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 369 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 193 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 HIS F 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.089976 restraints weight = 103047.530| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 5.89 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17088 Z= 0.106 Angle : 0.515 14.534 23244 Z= 0.267 Chirality : 0.043 0.149 2664 Planarity : 0.005 0.071 2958 Dihedral : 4.104 49.884 2432 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.49 % Allowed : 19.92 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.18), residues: 2208 helix: 1.68 (0.17), residues: 966 sheet: 1.22 (0.28), residues: 372 loop : 0.01 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 147 TYR 0.015 0.001 TYR F 198 PHE 0.007 0.001 PHE E 200 TRP 0.031 0.002 TRP B 356 HIS 0.006 0.000 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00245 (17082) covalent geometry : angle 0.51448 (23226) hydrogen bonds : bond 0.02882 ( 846) hydrogen bonds : angle 4.43524 ( 2322) link_TRANS : bond 0.00153 ( 6) link_TRANS : angle 0.68527 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2970.32 seconds wall clock time: 52 minutes 5.81 seconds (3125.81 seconds total)