Starting phenix.real_space_refine on Tue Jan 21 09:29:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c21_45135/01_2025/9c21_45135_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c21_45135/01_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_45135/01_2025/9c21_45135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c21_45135/01_2025/9c21_45135.map" model { file = "/net/cci-nas-00/data/ceres_data/9c21_45135/01_2025/9c21_45135_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c21_45135/01_2025/9c21_45135_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 1, 'HIC:plan-2': 1, 'ASP:plan': 8} 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: {'GLN:plan1': 1, 'HIC:plan-2': 1, 'HIC:plan-1': 1, 'ASP:plan': 8, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 91 bond proxies already assigned to first conformer: 2823 Restraints were copied for chains: C, B, E, D, 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: 7.77, per 1000 atoms: 0.47 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: 4.08 Conformation dependent library (CDL) restraints added in 4.0 seconds 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: 2.51 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: 5.80 Time building geometry restraints manager: 4.71 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.950 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.680 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.590 ------------------------------------------------------------------------------- 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 17082 Z= 0.304 Angle : 0.714 10.600 23226 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 : 12.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.002 TRP A 356 HIS 0.002 0.000 BHIS B 73 PHE 0.009 0.001 PHE B 279 TYR 0.009 0.001 TYR D 362 ARG 0.003 0.000 ARG C 177 *********************** 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 : 1.799 Fit side-chains REVERT: A 370 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7215 (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: 0.7612 (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: 0.8309 (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: 0.8572 (m) outliers start: 24 outliers final: 14 residues processed: 298 average time/residue: 0.2276 time to fit residues: 111.3739 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 : 1.774 ------------------------------------------------------------------------------- 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 187 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.106082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.088054 restraints weight = 106579.048| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 5.87 r_work (final): 0.3135 ------------------------------------------------------------------------------- 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 = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17082 Z= 0.303 Angle : 0.594 7.884 23226 Z= 0.314 Chirality : 0.046 0.156 2664 Planarity : 0.006 0.087 2958 Dihedral : 5.134 46.356 2445 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.01 % Allowed : 17.61 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 2208 helix: 1.33 (0.18), residues: 966 sheet: 0.85 (0.27), residues: 366 loop : -0.34 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 356 HIS 0.008 0.001 HIS E 371 PHE 0.035 0.001 PHE F 279 TYR 0.017 0.001 TYR C 306 ARG 0.004 0.000 ARG E 116 *********************** 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 268 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 2.025 Fit side-chains REVERT: B 119 MET cc_start: 0.8407 (ttm) cc_final: 0.8202 (ttm) REVERT: C 94 LEU cc_start: 0.9235 (mp) cc_final: 0.8868 (mt) REVERT: D 82 MET cc_start: 0.8023 (tpp) cc_final: 0.7741 (ttp) REVERT: D 222 ASP cc_start: 0.7605 (p0) cc_final: 0.6915 (p0) REVERT: D 227 MET cc_start: 0.8284 (mmm) cc_final: 0.7568 (tpt) REVERT: D 313 MET cc_start: 0.8693 (ttm) cc_final: 0.8153 (ttt) REVERT: E 78 ASN cc_start: 0.7728 (t0) cc_final: 0.7098 (t0) REVERT: F 279 PHE cc_start: 0.6666 (t80) cc_final: 0.6456 (t80) outliers start: 51 outliers final: 37 residues processed: 256 average time/residue: 0.2300 time to fit residues: 96.9870 Evaluate side-chains 233 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.809 ------------------------------------------------------------------------------- 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 123 MET Chi-restraints excluded: chain F residue 152 VAL 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 51 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.111254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094036 restraints weight = 98017.124| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 5.32 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17082 Z= 0.174 Angle : 0.527 9.757 23226 Z= 0.274 Chirality : 0.043 0.133 2664 Planarity : 0.005 0.073 2958 Dihedral : 4.344 44.364 2438 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.37 % Allowed : 17.79 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.18), residues: 2208 helix: 1.46 (0.18), residues: 966 sheet: 1.11 (0.27), residues: 366 loop : -0.17 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 356 HIS 0.003 0.000 HIS E 371 PHE 0.017 0.001 PHE F 279 TYR 0.017 0.001 TYR A 143 ARG 0.003 0.000 ARG F 147 *********************** 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 282 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 1.826 Fit side-chains REVERT: A 117 GLU cc_start: 0.6804 (tp30) cc_final: 0.6470 (tp30) REVERT: A 222 ASP cc_start: 0.7339 (p0) cc_final: 0.6669 (p0) REVERT: C 94 LEU cc_start: 0.9188 (mp) cc_final: 0.8840 (mt) REVERT: D 82 MET cc_start: 0.8191 (tpp) cc_final: 0.7780 (tpp) REVERT: D 222 ASP cc_start: 0.7268 (p0) cc_final: 0.6734 (p0) REVERT: D 227 MET cc_start: 0.8567 (mmm) cc_final: 0.7872 (tpt) REVERT: E 159 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8266 (m) REVERT: F 163 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8205 (p) REVERT: F 227 MET cc_start: 0.8353 (mmm) cc_final: 0.7816 (tpp) outliers start: 57 outliers final: 42 residues processed: 268 average time/residue: 0.2211 time to fit residues: 98.9278 Evaluate side-chains 251 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 1.910 ------------------------------------------------------------------------------- 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 A residue 369 ILE 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 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 152 VAL Chi-restraints excluded: chain F residue 163 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 93 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.112086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094920 restraints weight = 95528.885| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 5.28 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17082 Z= 0.160 Angle : 0.502 8.699 23226 Z= 0.263 Chirality : 0.043 0.139 2664 Planarity : 0.005 0.064 2958 Dihedral : 4.067 44.108 2434 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.37 % Allowed : 17.91 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2208 helix: 1.58 (0.17), residues: 966 sheet: 1.21 (0.27), residues: 372 loop : -0.05 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 356 HIS 0.002 0.000 HIS E 371 PHE 0.007 0.001 PHE B 352 TYR 0.016 0.001 TYR D 143 ARG 0.003 0.000 ARG F 147 *********************** 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 283 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 1.765 Fit side-chains REVERT: A 117 GLU cc_start: 0.6555 (tp30) cc_final: 0.6132 (tp30) REVERT: A 132 MET cc_start: 0.8762 (tmm) cc_final: 0.8475 (tmm) REVERT: A 222 ASP cc_start: 0.7101 (p0) cc_final: 0.6460 (p0) REVERT: C 94 LEU cc_start: 0.9191 (mp) cc_final: 0.8852 (mt) REVERT: C 207 GLU cc_start: 0.7770 (tp30) cc_final: 0.7487 (tp30) REVERT: D 222 ASP cc_start: 0.7046 (p0) cc_final: 0.6476 (p0) REVERT: E 159 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8255 (m) REVERT: F 227 MET cc_start: 0.8181 (mmm) cc_final: 0.7655 (tpp) outliers start: 57 outliers final: 48 residues processed: 269 average time/residue: 0.2188 time to fit residues: 98.3215 Evaluate side-chains 255 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 1.984 ------------------------------------------------------------------------------- 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 71 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 A residue 369 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 152 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 12 ASN 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 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 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 369 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 152 optimal weight: 0.2980 chunk 147 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN F 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090941 restraints weight = 100742.661| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 5.54 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17082 Z= 0.308 Angle : 0.575 12.190 23226 Z= 0.302 Chirality : 0.046 0.140 2664 Planarity : 0.005 0.065 2958 Dihedral : 4.520 44.913 2434 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.96 % Allowed : 18.14 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2208 helix: 1.52 (0.17), residues: 966 sheet: 1.13 (0.28), residues: 372 loop : -0.15 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 356 HIS 0.007 0.001 HIS D 101 PHE 0.041 0.002 PHE F 279 TYR 0.017 0.001 TYR A 143 ARG 0.004 0.000 ARG C 116 *********************** 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 270 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 203 time to evaluate : 1.873 Fit side-chains REVERT: A 153 MET cc_start: 0.7862 (tmm) cc_final: 0.7548 (tmm) REVERT: D 241 GLU cc_start: 0.8007 (tp30) cc_final: 0.7662 (tt0) REVERT: E 78 ASN cc_start: 0.7890 (t0) cc_final: 0.7083 (t0) REVERT: E 159 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8152 (m) REVERT: F 279 PHE cc_start: 0.6473 (t80) cc_final: 0.6223 (t80) outliers start: 67 outliers final: 59 residues processed: 259 average time/residue: 0.2256 time to fit residues: 98.1811 Evaluate side-chains 250 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 1.758 ------------------------------------------------------------------------------- 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 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 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 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 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 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 70 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 5 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.104242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.087987 restraints weight = 108055.994| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 5.46 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17082 Z= 0.229 Angle : 0.552 13.058 23226 Z= 0.286 Chirality : 0.044 0.140 2664 Planarity : 0.005 0.061 2958 Dihedral : 4.407 46.064 2434 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.02 % Allowed : 18.14 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2208 helix: 1.52 (0.17), residues: 966 sheet: 1.13 (0.28), residues: 372 loop : -0.13 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 356 HIS 0.007 0.001 HIS D 101 PHE 0.029 0.001 PHE F 279 TYR 0.014 0.001 TYR A 143 ARG 0.002 0.000 ARG D 116 *********************** 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 276 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 208 time to evaluate : 1.977 Fit side-chains REVERT: A 117 GLU cc_start: 0.6730 (tp30) cc_final: 0.6276 (tp30) REVERT: A 153 MET cc_start: 0.7697 (tmm) cc_final: 0.7360 (tmm) REVERT: C 207 GLU cc_start: 0.7847 (tp30) cc_final: 0.7463 (tp30) REVERT: D 227 MET cc_start: 0.8275 (mmm) cc_final: 0.7532 (tpt) REVERT: E 159 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8107 (m) REVERT: F 279 PHE cc_start: 0.6426 (t80) cc_final: 0.6191 (t80) outliers start: 68 outliers final: 62 residues processed: 265 average time/residue: 0.2394 time to fit residues: 106.3319 Evaluate side-chains 262 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 199 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 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 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 305 MET 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 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 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 214 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 112 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.104956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.087427 restraints weight = 95836.417| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 5.79 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17082 Z= 0.188 Angle : 0.530 13.913 23226 Z= 0.274 Chirality : 0.044 0.137 2664 Planarity : 0.004 0.058 2958 Dihedral : 4.283 47.380 2434 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.90 % Allowed : 18.50 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2208 helix: 1.58 (0.17), residues: 966 sheet: 1.13 (0.28), residues: 372 loop : -0.02 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 356 HIS 0.004 0.001 HIS D 101 PHE 0.024 0.001 PHE F 279 TYR 0.024 0.001 TYR D 143 ARG 0.002 0.000 ARG F 147 *********************** 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 280 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 1.948 Fit side-chains REVERT: A 153 MET cc_start: 0.7630 (tmm) cc_final: 0.7289 (tmm) REVERT: D 227 MET cc_start: 0.8263 (mmm) cc_final: 0.7506 (tpt) REVERT: E 159 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.8057 (m) REVERT: F 279 PHE cc_start: 0.6323 (t80) cc_final: 0.6083 (t80) outliers start: 66 outliers final: 63 residues processed: 267 average time/residue: 0.2310 time to fit residues: 105.0107 Evaluate side-chains 266 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 202 time to evaluate : 1.851 ------------------------------------------------------------------------------- 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 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 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 305 MET 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 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 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 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 40 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.102006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.084307 restraints weight = 113783.624| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 6.03 r_work: 0.2874 rms_B_bonded: 5.99 restraints_weight: 2.0000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17082 Z= 0.289 Angle : 0.579 15.080 23226 Z= 0.300 Chirality : 0.045 0.142 2664 Planarity : 0.005 0.059 2958 Dihedral : 4.607 48.747 2434 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.90 % Allowed : 18.56 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2208 helix: 1.52 (0.17), residues: 966 sheet: 1.07 (0.28), residues: 372 loop : -0.10 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 356 HIS 0.005 0.001 HIS F 101 PHE 0.022 0.001 PHE F 279 TYR 0.016 0.001 TYR A 169 ARG 0.003 0.000 ARG F 116 *********************** 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 263 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 1.929 Fit side-chains REVERT: A 153 MET cc_start: 0.8223 (tmm) cc_final: 0.7887 (tmm) REVERT: C 143 TYR cc_start: 0.6887 (m-80) cc_final: 0.6480 (m-10) REVERT: E 159 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8255 (m) REVERT: F 279 PHE cc_start: 0.6681 (t80) cc_final: 0.6410 (t80) outliers start: 66 outliers final: 62 residues processed: 253 average time/residue: 0.2200 time to fit residues: 94.0599 Evaluate side-chains 258 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 195 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 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 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 305 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 180 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 201 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 137 optimal weight: 0.0010 chunk 9 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.106367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.088772 restraints weight = 100065.381| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 5.80 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17082 Z= 0.157 Angle : 0.522 14.418 23226 Z= 0.270 Chirality : 0.043 0.137 2664 Planarity : 0.005 0.057 2958 Dihedral : 4.086 49.910 2432 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.61 % Allowed : 19.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.18), residues: 2208 helix: 1.65 (0.17), residues: 960 sheet: 1.16 (0.28), residues: 372 loop : -0.05 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 356 HIS 0.006 0.001 HIS F 101 PHE 0.020 0.001 PHE F 279 TYR 0.024 0.001 TYR D 143 ARG 0.002 0.000 ARG F 147 *********************** 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: 61 poor density : 217 time to evaluate : 1.871 Fit side-chains REVERT: A 117 GLU cc_start: 0.6695 (tp30) cc_final: 0.6268 (tp30) REVERT: A 153 MET cc_start: 0.7607 (tmm) cc_final: 0.7252 (tmm) REVERT: C 143 TYR cc_start: 0.6827 (m-80) cc_final: 0.6403 (m-10) REVERT: C 227 MET cc_start: 0.8442 (mmm) cc_final: 0.7857 (tpp) REVERT: D 227 MET cc_start: 0.8309 (mmm) cc_final: 0.7549 (tpt) REVERT: E 159 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8149 (m) REVERT: F 279 PHE cc_start: 0.6474 (t80) cc_final: 0.6201 (t80) outliers start: 61 outliers final: 57 residues processed: 263 average time/residue: 0.2297 time to fit residues: 101.0187 Evaluate side-chains 268 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 210 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 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 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 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 41 optimal weight: 4.9990 chunk 220 optimal weight: 0.0030 chunk 219 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.107717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.089142 restraints weight = 124783.119| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 6.42 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.002 0.031 17082 Z= 0.154 Angle : 0.521 14.749 23226 Z= 0.267 Chirality : 0.043 0.149 2664 Planarity : 0.005 0.055 2958 Dihedral : 4.039 49.944 2432 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.31 % Allowed : 19.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2208 helix: 1.72 (0.17), residues: 960 sheet: 1.20 (0.28), residues: 372 loop : 0.03 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 356 HIS 0.008 0.001 HIS F 101 PHE 0.019 0.001 PHE F 279 TYR 0.014 0.001 TYR A 143 ARG 0.002 0.000 ARG F 147 ********************** 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 281 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 1.912 Fit side-chains REVERT: A 117 GLU cc_start: 0.6660 (tp30) cc_final: 0.6244 (tp30) REVERT: A 153 MET cc_start: 0.7563 (tmm) cc_final: 0.7222 (tmm) REVERT: A 178 LEU cc_start: 0.8087 (tp) cc_final: 0.7767 (tp) REVERT: A 283 MET cc_start: 0.8375 (mmm) cc_final: 0.8123 (mmm) REVERT: B 119 MET cc_start: 0.8501 (ttm) cc_final: 0.8280 (ttm) REVERT: C 143 TYR cc_start: 0.6793 (m-80) cc_final: 0.6359 (m-10) REVERT: C 227 MET cc_start: 0.8431 (mmm) cc_final: 0.7843 (tpp) REVERT: E 132 MET cc_start: 0.8474 (tmm) cc_final: 0.8211 (tmm) REVERT: E 159 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8182 (m) outliers start: 56 outliers final: 54 residues processed: 266 average time/residue: 0.2237 time to fit residues: 102.0917 Evaluate side-chains 270 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 215 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 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 17 CYS 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 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 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 E residue 12 ASN 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 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 136 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 9 optimal weight: 0.0670 chunk 140 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 174 optimal weight: 0.0980 chunk 159 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN F 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.089591 restraints weight = 123135.543| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 6.48 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17082 Z= 0.139 Angle : 0.516 14.620 23226 Z= 0.265 Chirality : 0.043 0.152 2664 Planarity : 0.005 0.069 2958 Dihedral : 3.974 50.085 2432 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.07 % Allowed : 19.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2208 helix: 1.76 (0.17), residues: 960 sheet: 1.24 (0.28), residues: 372 loop : 0.08 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 356 HIS 0.004 0.000 HIS F 101 PHE 0.007 0.001 PHE A 279 TYR 0.012 0.001 TYR D 198 ARG 0.002 0.000 ARG F 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5615.44 seconds wall clock time: 102 minutes 33.95 seconds (6153.95 seconds total)