Starting phenix.real_space_refine on Sun Aug 24 06:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ny2_49916/08_2025/9ny2_49916.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ny2_49916/08_2025/9ny2_49916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ny2_49916/08_2025/9ny2_49916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ny2_49916/08_2025/9ny2_49916.map" model { file = "/net/cci-nas-00/data/ceres_data/9ny2_49916/08_2025/9ny2_49916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ny2_49916/08_2025/9ny2_49916.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.007 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 84 5.16 5 C 10703 2.51 5 N 3010 2.21 5 O 3402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17199 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2457 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2457 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2457 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "D" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2457 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "E" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2457 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "F" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2457 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "G" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2457 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Time building chain proxies: 3.79, per 1000 atoms: 0.22 Number of scatterers: 17199 At special positions: 0 Unit cell: (175.956, 200.552, 136.224, 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 84 16.00 O 3402 8.00 N 3010 7.00 C 10703 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 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 740.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 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: 56 helices and 29 sheets defined 23.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 96 through 99 Processing helix chain 'A' and resid 107 through 130 removed outlier: 3.562A pdb=" N TYR A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.049A pdb=" N LEU A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 218 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.619A pdb=" N GLY A 307 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 96 through 99 Processing helix chain 'B' and resid 107 through 130 removed outlier: 3.699A pdb=" N TYR B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 183 through 197 removed outlier: 4.044A pdb=" N LEU B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 217 Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.537A pdb=" N SER B 306 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.583A pdb=" N LYS C 99 " --> pdb=" O GLY C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 130 removed outlier: 3.738A pdb=" N LYS C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 183 through 198 removed outlier: 3.927A pdb=" N LEU C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.638A pdb=" N GLY C 307 " --> pdb=" O GLU C 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.757A pdb=" N LYS D 99 " --> pdb=" O GLY D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 130 removed outlier: 3.606A pdb=" N TYR D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 183 through 197 removed outlier: 4.138A pdb=" N LEU D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 303 through 307 removed outlier: 3.504A pdb=" N SER D 306 " --> pdb=" O ASN D 303 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY D 307 " --> pdb=" O GLU D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 307' Processing helix chain 'E' and resid 32 through 38 Processing helix chain 'E' and resid 95 through 100 removed outlier: 3.882A pdb=" N LYS E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 95 through 100' Processing helix chain 'E' and resid 107 through 130 removed outlier: 3.567A pdb=" N TYR E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.941A pdb=" N LEU E 187 " --> pdb=" O THR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 218 Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 303 through 307 removed outlier: 3.625A pdb=" N GLY E 307 " --> pdb=" O GLU E 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 38 Processing helix chain 'F' and resid 95 through 100 removed outlier: 3.719A pdb=" N LYS F 99 " --> pdb=" O GLY F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 130 removed outlier: 3.720A pdb=" N TYR F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 121 " --> pdb=" O SER F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 152 Processing helix chain 'F' and resid 183 through 197 removed outlier: 4.005A pdb=" N LEU F 187 " --> pdb=" O THR F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 217 Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.565A pdb=" N SER F 306 " --> pdb=" O ASN F 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 38 Processing helix chain 'G' and resid 96 through 99 Processing helix chain 'G' and resid 107 through 130 removed outlier: 3.925A pdb=" N TYR G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'G' and resid 183 through 198 removed outlier: 3.931A pdb=" N LEU G 187 " --> pdb=" O THR G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 217 Processing helix chain 'G' and resid 265 through 267 No H-bonds generated for 'chain 'G' and resid 265 through 267' Processing helix chain 'G' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 25 removed outlier: 8.385A pdb=" N ILE A 21 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLU C 49 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE A 23 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN C 51 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 25 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 42 removed outlier: 6.843A pdb=" N GLU A 296 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 294 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 278 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLN A 292 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N HIS A 280 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LYS A 290 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 83 removed outlier: 13.869A pdb=" N THR A 47 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 13.771A pdb=" N ILE B 23 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N GLU A 49 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N TYR B 25 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN A 51 " --> pdb=" O TYR B 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.083A pdb=" N ARG A 180 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.515A pdb=" N THR A 206 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 226 removed outlier: 3.584A pdb=" N LEU B 227 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 233 through 235 removed outlier: 6.234A pdb=" N ILE A 234 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 206 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 42 removed outlier: 6.603A pdb=" N GLY B 39 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N TYR B 273 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY B 41 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ARG B 275 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU B 296 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B 294 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE B 278 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN B 292 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N HIS B 280 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LYS B 290 " --> pdb=" O HIS B 280 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 82 removed outlier: 9.866A pdb=" N GLU B 49 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N TYR F 25 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLN B 51 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 180 through 181 removed outlier: 5.929A pdb=" N ARG B 180 " --> pdb=" O VAL B 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.510A pdb=" N THR B 206 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 240 " --> pdb=" O ILE F 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 20 through 25 removed outlier: 8.224A pdb=" N ILE C 21 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLU D 49 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE C 23 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN D 51 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 42 removed outlier: 6.752A pdb=" N GLY C 39 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N TYR C 273 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY C 41 " --> pdb=" O TYR C 273 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ARG C 275 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N CYS C 272 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ARG C 300 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU C 274 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N THR C 298 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU C 296 " --> pdb=" O PRO C 276 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 180 through 181 removed outlier: 5.743A pdb=" N ARG C 180 " --> pdb=" O VAL C 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 226 through 228 removed outlier: 5.988A pdb=" N LEU C 227 " --> pdb=" O THR D 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 233 through 235 Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 25 removed outlier: 6.759A pdb=" N ASP D 19 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLN E 51 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ILE D 21 " --> pdb=" O GLN E 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.840A pdb=" N GLY D 39 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYR D 273 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY D 41 " --> pdb=" O TYR D 273 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ARG D 275 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU D 296 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU D 294 " --> pdb=" O PRO D 276 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE D 278 " --> pdb=" O GLN D 292 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLN D 292 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N HIS D 280 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LYS D 290 " --> pdb=" O HIS D 280 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 180 through 181 removed outlier: 6.217A pdb=" N ARG D 180 " --> pdb=" O VAL D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 233 through 236 removed outlier: 3.523A pdb=" N THR E 206 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 20 through 25 removed outlier: 8.668A pdb=" N ILE E 21 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLU F 49 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE E 23 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN F 51 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 39 through 42 removed outlier: 6.859A pdb=" N GLU E 296 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU E 294 " --> pdb=" O PRO E 276 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE E 278 " --> pdb=" O GLN E 292 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLN E 292 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N HIS E 280 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS E 290 " --> pdb=" O HIS E 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 233 through 234 removed outlier: 6.866A pdb=" N ILE E 234 " --> pdb=" O GLU F 242 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 206 " --> pdb=" O ARG F 251 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 39 through 42 removed outlier: 6.813A pdb=" N GLU F 296 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU F 294 " --> pdb=" O PRO F 276 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE F 278 " --> pdb=" O GLN F 292 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN F 292 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N HIS F 280 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LYS F 290 " --> pdb=" O HIS F 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 180 through 181 removed outlier: 6.193A pdb=" N ARG F 180 " --> pdb=" O VAL F 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'G' and resid 39 through 42 removed outlier: 6.684A pdb=" N GLU G 296 " --> pdb=" O LEU G 274 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU G 294 " --> pdb=" O PRO G 276 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE G 278 " --> pdb=" O GLN G 292 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN G 292 " --> pdb=" O PHE G 278 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N HIS G 280 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS G 290 " --> pdb=" O HIS G 280 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 47 through 52 Processing sheet with id=AD1, first strand: chain 'G' and resid 180 through 181 removed outlier: 5.965A pdb=" N ARG G 180 " --> pdb=" O VAL G 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 240 through 242 560 hydrogen bonds defined for protein. 1506 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: 2.18 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5816 1.35 - 1.47: 3842 1.47 - 1.59: 7653 1.59 - 1.71: 0 1.71 - 1.83: 154 Bond restraints: 17465 Sorted by residual: bond pdb=" CB LYS D 101 " pdb=" CG LYS D 101 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" CB LYS A 101 " pdb=" CG LYS A 101 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" CA LYS G 72 " pdb=" CB LYS G 72 " ideal model delta sigma weight residual 1.531 1.567 -0.036 3.12e-02 1.03e+03 1.37e+00 bond pdb=" CG MET C 1 " pdb=" SD MET C 1 " ideal model delta sigma weight residual 1.803 1.831 -0.028 2.50e-02 1.60e+03 1.30e+00 bond pdb=" CB LYS G 72 " pdb=" CG LYS G 72 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 ... (remaining 17460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 23399 2.40 - 4.80: 185 4.80 - 7.20: 18 7.20 - 9.60: 1 9.60 - 12.00: 1 Bond angle restraints: 23604 Sorted by residual: angle pdb=" CB MET C 218 " pdb=" CG MET C 218 " pdb=" SD MET C 218 " ideal model delta sigma weight residual 112.70 124.70 -12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CA LYS A 101 " pdb=" CB LYS A 101 " pdb=" CG LYS A 101 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CA LYS D 101 " pdb=" CB LYS D 101 " pdb=" CG LYS D 101 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.17e+01 angle pdb=" C THR A 5 " pdb=" CA THR A 5 " pdb=" CB THR A 5 " ideal model delta sigma weight residual 110.42 116.71 -6.29 1.99e+00 2.53e-01 9.98e+00 angle pdb=" CG ARG E 251 " pdb=" CD ARG E 251 " pdb=" NE ARG E 251 " ideal model delta sigma weight residual 112.00 118.80 -6.80 2.20e+00 2.07e-01 9.54e+00 ... (remaining 23599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 9066 17.62 - 35.25: 1135 35.25 - 52.87: 326 52.87 - 70.50: 77 70.50 - 88.12: 29 Dihedral angle restraints: 10633 sinusoidal: 4235 harmonic: 6398 Sorted by residual: dihedral pdb=" CA PRO F 4 " pdb=" C PRO F 4 " pdb=" N THR F 5 " pdb=" CA THR F 5 " ideal model delta harmonic sigma weight residual 180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA SER C 9 " pdb=" C SER C 9 " pdb=" N THR C 10 " pdb=" CA THR C 10 " ideal model delta harmonic sigma weight residual 180.00 156.57 23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ASN G 107 " pdb=" C ASN G 107 " pdb=" N GLU G 108 " pdb=" CA GLU G 108 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 10630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1808 0.032 - 0.064: 576 0.064 - 0.096: 173 0.096 - 0.128: 119 0.128 - 0.160: 5 Chirality restraints: 2681 Sorted by residual: chirality pdb=" CB THR A 5 " pdb=" CA THR A 5 " pdb=" OG1 THR A 5 " pdb=" CG2 THR A 5 " both_signs ideal model delta sigma weight residual False 2.55 2.71 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CB THR B 5 " pdb=" CA THR B 5 " pdb=" OG1 THR B 5 " pdb=" CG2 THR B 5 " both_signs ideal model delta sigma weight residual False 2.55 2.69 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE E 263 " pdb=" N ILE E 263 " pdb=" C ILE E 263 " pdb=" CB ILE E 263 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 2678 not shown) Planarity restraints: 3080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 281 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" CD GLU E 281 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU E 281 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU E 281 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 10 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C THR C 10 " 0.032 2.00e-02 2.50e+03 pdb=" O THR C 10 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL C 11 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 3 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO D 4 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 4 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 4 " 0.020 5.00e-02 4.00e+02 ... (remaining 3077 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 424 2.69 - 3.24: 15629 3.24 - 3.79: 24904 3.79 - 4.35: 33477 4.35 - 4.90: 57701 Nonbonded interactions: 132135 Sorted by model distance: nonbonded pdb=" O GLU E 224 " pdb=" OG1 THR F 223 " model vdw 2.136 3.040 nonbonded pdb=" OG SER B 75 " pdb=" NZ LYS F 115 " model vdw 2.161 3.120 nonbonded pdb=" O GLU C 224 " pdb=" OG1 THR D 223 " model vdw 2.172 3.040 nonbonded pdb=" OG1 THR A 223 " pdb=" O GLU B 224 " model vdw 2.185 3.040 nonbonded pdb=" N GLU B 281 " pdb=" OE1 GLU B 281 " model vdw 2.197 3.120 ... (remaining 132130 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.550 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 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 : 0.003 0.039 17465 Z= 0.125 Angle : 0.530 12.002 23604 Z= 0.295 Chirality : 0.040 0.160 2681 Planarity : 0.003 0.043 3080 Dihedral : 17.656 88.122 6517 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.54 % Favored : 96.05 % Rotamer: Outliers : 1.63 % Allowed : 25.64 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2205 helix: 2.43 (0.26), residues: 394 sheet: 0.43 (0.20), residues: 630 loop : -0.72 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 251 TYR 0.012 0.001 TYR F 111 PHE 0.011 0.001 PHE D 277 TRP 0.006 0.001 TRP E 50 HIS 0.003 0.001 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00261 (17465) covalent geometry : angle 0.53015 (23604) hydrogen bonds : bond 0.16058 ( 560) hydrogen bonds : angle 5.35155 ( 1506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.703 Fit side-chains REVERT: A 12 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.3761 (tp30) REVERT: B 76 PHE cc_start: 0.8801 (m-10) cc_final: 0.8557 (m-10) REVERT: D 101 LYS cc_start: 0.6449 (pptt) cc_final: 0.5981 (pptt) outliers start: 30 outliers final: 22 residues processed: 163 average time/residue: 0.5476 time to fit residues: 99.7503 Evaluate side-chains 151 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 79 MET Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 217 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 ASN B 197 ASN B 316 GLN C 107 ASN C 217 ASN D 6 ASN D 156 ASN D 197 ASN E 236 GLN G 85 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.052034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.042421 restraints weight = 52665.855| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 2.95 r_work: 0.2484 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2376 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17465 Z= 0.220 Angle : 0.551 7.700 23604 Z= 0.306 Chirality : 0.043 0.141 2681 Planarity : 0.003 0.037 3080 Dihedral : 5.888 78.750 2429 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.26 % Favored : 95.28 % Rotamer: Outliers : 2.23 % Allowed : 23.47 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.17), residues: 2205 helix: 2.22 (0.26), residues: 403 sheet: 0.38 (0.20), residues: 614 loop : -0.90 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 251 TYR 0.014 0.001 TYR D 111 PHE 0.015 0.001 PHE B 76 TRP 0.007 0.001 TRP D 255 HIS 0.005 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00513 (17465) covalent geometry : angle 0.55077 (23604) hydrogen bonds : bond 0.05833 ( 560) hydrogen bonds : angle 5.43305 ( 1506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.696 Fit side-chains REVERT: A 5 THR cc_start: 0.8283 (m) cc_final: 0.8061 (t) REVERT: A 12 GLU cc_start: 0.5054 (OUTLIER) cc_final: 0.3164 (tt0) REVERT: A 68 ASP cc_start: 0.8162 (m-30) cc_final: 0.6457 (p0) REVERT: B 5 THR cc_start: 0.8231 (m) cc_final: 0.7997 (p) REVERT: B 180 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8140 (ptt90) REVERT: C 218 MET cc_start: 0.8493 (tpp) cc_final: 0.8153 (tpp) REVERT: D 101 LYS cc_start: 0.6201 (pptt) cc_final: 0.5712 (pptt) REVERT: F 22 ASP cc_start: 0.9214 (OUTLIER) cc_final: 0.8876 (t0) REVERT: F 101 LYS cc_start: 0.6164 (mptt) cc_final: 0.5820 (mptt) REVERT: F 289 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8739 (mm-30) REVERT: G 289 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8421 (tm-30) outliers start: 41 outliers final: 12 residues processed: 153 average time/residue: 0.6263 time to fit residues: 105.7506 Evaluate side-chains 130 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 289 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 178 optimal weight: 30.0000 chunk 7 optimal weight: 20.0000 chunk 216 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 192 optimal weight: 0.0770 chunk 97 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 overall best weight: 4.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN C 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.053422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.043672 restraints weight = 52977.140| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 3.02 r_work: 0.2521 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17465 Z= 0.119 Angle : 0.475 7.054 23604 Z= 0.265 Chirality : 0.041 0.140 2681 Planarity : 0.003 0.038 3080 Dihedral : 5.406 77.121 2404 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.85 % Favored : 95.74 % Rotamer: Outliers : 2.06 % Allowed : 23.52 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.17), residues: 2205 helix: 2.25 (0.26), residues: 403 sheet: 0.42 (0.20), residues: 609 loop : -0.84 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 251 TYR 0.012 0.001 TYR B 111 PHE 0.007 0.001 PHE B 76 TRP 0.005 0.001 TRP G 50 HIS 0.002 0.001 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00259 (17465) covalent geometry : angle 0.47525 (23604) hydrogen bonds : bond 0.04606 ( 560) hydrogen bonds : angle 5.14024 ( 1506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.680 Fit side-chains REVERT: A 5 THR cc_start: 0.8467 (m) cc_final: 0.8258 (t) REVERT: B 5 THR cc_start: 0.8420 (m) cc_final: 0.8190 (p) REVERT: D 101 LYS cc_start: 0.6176 (pptt) cc_final: 0.5672 (pptt) REVERT: F 101 LYS cc_start: 0.5926 (mptt) cc_final: 0.5454 (mptt) REVERT: F 289 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8787 (mm-30) outliers start: 38 outliers final: 10 residues processed: 145 average time/residue: 0.6618 time to fit residues: 106.3958 Evaluate side-chains 121 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 203 optimal weight: 30.0000 chunk 6 optimal weight: 40.0000 chunk 146 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 178 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 44 optimal weight: 30.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN C 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.052221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.042683 restraints weight = 52577.357| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 2.96 r_work: 0.2486 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2376 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17465 Z= 0.176 Angle : 0.509 9.308 23604 Z= 0.282 Chirality : 0.042 0.140 2681 Planarity : 0.003 0.043 3080 Dihedral : 5.301 80.304 2398 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.26 % Favored : 95.33 % Rotamer: Outliers : 2.55 % Allowed : 22.87 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.17), residues: 2205 helix: 2.24 (0.26), residues: 403 sheet: 0.36 (0.20), residues: 614 loop : -0.87 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 251 TYR 0.011 0.001 TYR D 111 PHE 0.011 0.001 PHE B 76 TRP 0.006 0.001 TRP F 255 HIS 0.003 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00405 (17465) covalent geometry : angle 0.50926 (23604) hydrogen bonds : bond 0.05266 ( 560) hydrogen bonds : angle 5.22813 ( 1506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 0.736 Fit side-chains REVERT: B 5 THR cc_start: 0.8891 (m) cc_final: 0.8659 (p) REVERT: D 101 LYS cc_start: 0.6162 (pptt) cc_final: 0.5811 (pptt) REVERT: D 184 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8825 (mt-10) REVERT: E 101 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.8645 (mptt) REVERT: F 22 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8823 (t0) REVERT: F 101 LYS cc_start: 0.6096 (mptt) cc_final: 0.5712 (mptt) outliers start: 47 outliers final: 19 residues processed: 145 average time/residue: 0.5893 time to fit residues: 94.7113 Evaluate side-chains 132 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 79 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 100 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 209 optimal weight: 0.0670 chunk 202 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 overall best weight: 9.8132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN C 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.051280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.041661 restraints weight = 52186.749| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 3.00 r_work: 0.2450 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2341 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17465 Z= 0.235 Angle : 0.551 10.724 23604 Z= 0.303 Chirality : 0.043 0.276 2681 Planarity : 0.003 0.049 3080 Dihedral : 5.481 82.872 2398 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.40 % Favored : 95.15 % Rotamer: Outliers : 2.93 % Allowed : 22.22 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.17), residues: 2205 helix: 2.13 (0.26), residues: 403 sheet: 0.31 (0.20), residues: 594 loop : -0.98 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 251 TYR 0.012 0.001 TYR B 111 PHE 0.013 0.001 PHE B 76 TRP 0.006 0.001 TRP G 50 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00549 (17465) covalent geometry : angle 0.55128 (23604) hydrogen bonds : bond 0.05740 ( 560) hydrogen bonds : angle 5.35043 ( 1506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 109 time to evaluate : 0.497 Fit side-chains REVERT: C 128 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.9089 (ttp) REVERT: D 101 LYS cc_start: 0.6271 (pptt) cc_final: 0.5853 (pptt) REVERT: E 101 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.8667 (mptt) REVERT: F 22 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8821 (t0) REVERT: G 281 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8405 (mm-30) REVERT: G 289 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: G 316 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8849 (pp30) outliers start: 54 outliers final: 18 residues processed: 151 average time/residue: 0.6250 time to fit residues: 104.5282 Evaluate side-chains 132 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 316 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN C 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.052083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.042690 restraints weight = 52380.725| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 2.93 r_work: 0.2482 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2373 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17465 Z= 0.171 Angle : 0.521 11.148 23604 Z= 0.284 Chirality : 0.042 0.219 2681 Planarity : 0.003 0.046 3080 Dihedral : 5.382 82.327 2398 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.35 % Favored : 95.24 % Rotamer: Outliers : 2.12 % Allowed : 23.25 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.17), residues: 2205 helix: 2.21 (0.26), residues: 403 sheet: 0.32 (0.20), residues: 594 loop : -0.94 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 251 TYR 0.013 0.001 TYR B 111 PHE 0.008 0.001 PHE B 76 TRP 0.006 0.001 TRP G 50 HIS 0.003 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00393 (17465) covalent geometry : angle 0.52106 (23604) hydrogen bonds : bond 0.05005 ( 560) hydrogen bonds : angle 5.14449 ( 1506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 158 SER cc_start: 0.9327 (OUTLIER) cc_final: 0.8762 (p) REVERT: C 128 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.9041 (ttp) REVERT: D 101 LYS cc_start: 0.6221 (pptt) cc_final: 0.5739 (pptt) REVERT: E 101 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.8627 (mptt) REVERT: F 22 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8749 (t0) REVERT: F 289 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8660 (mm-30) REVERT: G 281 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8260 (mm-30) REVERT: G 289 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.7954 (tm-30) outliers start: 39 outliers final: 19 residues processed: 139 average time/residue: 0.6115 time to fit residues: 94.2468 Evaluate side-chains 134 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 289 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 106 optimal weight: 0.3980 chunk 45 optimal weight: 7.9990 chunk 35 optimal weight: 0.1980 chunk 53 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 68 optimal weight: 40.0000 chunk 111 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN C 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.052879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.043281 restraints weight = 52198.293| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 2.97 r_work: 0.2512 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17465 Z= 0.119 Angle : 0.495 13.371 23604 Z= 0.268 Chirality : 0.041 0.195 2681 Planarity : 0.003 0.043 3080 Dihedral : 5.182 84.724 2397 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.04 % Favored : 95.56 % Rotamer: Outliers : 2.28 % Allowed : 23.25 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.17), residues: 2205 helix: 2.30 (0.26), residues: 403 sheet: 0.39 (0.20), residues: 609 loop : -0.83 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 251 TYR 0.012 0.001 TYR B 111 PHE 0.006 0.001 PHE E 76 TRP 0.006 0.001 TRP G 50 HIS 0.003 0.001 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00265 (17465) covalent geometry : angle 0.49493 (23604) hydrogen bonds : bond 0.04350 ( 560) hydrogen bonds : angle 4.93842 ( 1506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 158 SER cc_start: 0.9297 (OUTLIER) cc_final: 0.8759 (p) REVERT: D 101 LYS cc_start: 0.6037 (pptt) cc_final: 0.5079 (tmtt) REVERT: E 67 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8583 (tp30) REVERT: E 101 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8576 (mptt) REVERT: F 22 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8746 (t0) REVERT: F 101 LYS cc_start: 0.5991 (mptt) cc_final: 0.5522 (mptt) REVERT: F 289 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8627 (mm-30) REVERT: G 281 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8373 (mm-30) REVERT: G 289 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8115 (tm-30) outliers start: 42 outliers final: 18 residues processed: 145 average time/residue: 0.6267 time to fit residues: 100.7326 Evaluate side-chains 136 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 289 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 87 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 chunk 154 optimal weight: 2.9990 chunk 51 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 overall best weight: 8.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN C 217 ASN G 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.051649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.042231 restraints weight = 52672.468| |-----------------------------------------------------------------------------| r_work (start): 0.2583 rms_B_bonded: 2.95 r_work: 0.2467 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2358 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17465 Z= 0.199 Angle : 0.530 11.952 23604 Z= 0.289 Chirality : 0.042 0.176 2681 Planarity : 0.003 0.047 3080 Dihedral : 5.323 84.250 2397 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.35 % Favored : 95.24 % Rotamer: Outliers : 2.12 % Allowed : 23.79 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.17), residues: 2205 helix: 2.24 (0.26), residues: 403 sheet: 0.34 (0.20), residues: 594 loop : -0.93 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 251 TYR 0.011 0.001 TYR F 30 PHE 0.010 0.001 PHE B 76 TRP 0.006 0.001 TRP G 50 HIS 0.004 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00462 (17465) covalent geometry : angle 0.52951 (23604) hydrogen bonds : bond 0.05313 ( 560) hydrogen bonds : angle 5.14522 ( 1506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 0.594 Fit side-chains REVERT: A 158 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.8760 (p) REVERT: D 101 LYS cc_start: 0.6233 (pptt) cc_final: 0.5813 (pptt) REVERT: D 180 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8684 (ptt90) REVERT: E 67 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8599 (tp30) REVERT: E 101 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.8641 (mptt) REVERT: F 22 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8755 (t0) REVERT: F 101 LYS cc_start: 0.6133 (mptt) cc_final: 0.5812 (mptt) REVERT: F 289 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8665 (mm-30) REVERT: G 281 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8371 (mm-30) REVERT: G 289 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: G 316 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8527 (pp30) outliers start: 39 outliers final: 17 residues processed: 137 average time/residue: 0.6443 time to fit residues: 97.0849 Evaluate side-chains 130 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 316 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 198 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 180 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN C 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.052839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.043253 restraints weight = 51944.539| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 3.01 r_work: 0.2496 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2387 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17465 Z= 0.136 Angle : 0.505 12.449 23604 Z= 0.273 Chirality : 0.041 0.177 2681 Planarity : 0.003 0.052 3080 Dihedral : 5.246 85.696 2397 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.04 % Favored : 95.56 % Rotamer: Outliers : 1.47 % Allowed : 24.44 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.17), residues: 2205 helix: 2.28 (0.26), residues: 403 sheet: 0.35 (0.20), residues: 614 loop : -0.84 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 233 TYR 0.012 0.001 TYR B 111 PHE 0.007 0.001 PHE E 76 TRP 0.006 0.001 TRP G 50 HIS 0.003 0.001 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00306 (17465) covalent geometry : angle 0.50496 (23604) hydrogen bonds : bond 0.04640 ( 560) hydrogen bonds : angle 4.98144 ( 1506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.656 Fit side-chains REVERT: A 158 SER cc_start: 0.9316 (OUTLIER) cc_final: 0.8791 (p) REVERT: D 101 LYS cc_start: 0.6158 (pptt) cc_final: 0.5211 (tmtt) REVERT: E 101 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.8620 (mptt) REVERT: F 22 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8716 (t0) REVERT: F 101 LYS cc_start: 0.6056 (mptt) cc_final: 0.5375 (mptt) REVERT: F 289 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8673 (mm-30) REVERT: G 281 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8424 (mm-30) REVERT: G 289 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8027 (tm-30) outliers start: 27 outliers final: 15 residues processed: 131 average time/residue: 0.6198 time to fit residues: 89.6242 Evaluate side-chains 129 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 289 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 17 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 141 optimal weight: 0.0970 chunk 82 optimal weight: 40.0000 chunk 72 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 overall best weight: 4.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.052580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.042961 restraints weight = 52469.615| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 2.98 r_work: 0.2500 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17465 Z= 0.133 Angle : 0.495 12.841 23604 Z= 0.268 Chirality : 0.041 0.163 2681 Planarity : 0.003 0.052 3080 Dihedral : 5.183 87.305 2397 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.08 % Favored : 95.51 % Rotamer: Outliers : 1.36 % Allowed : 24.71 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.17), residues: 2205 helix: 2.31 (0.26), residues: 403 sheet: 0.39 (0.20), residues: 614 loop : -0.82 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 233 TYR 0.012 0.001 TYR B 111 PHE 0.007 0.001 PHE E 76 TRP 0.006 0.001 TRP G 50 HIS 0.003 0.001 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00300 (17465) covalent geometry : angle 0.49530 (23604) hydrogen bonds : bond 0.04540 ( 560) hydrogen bonds : angle 4.92260 ( 1506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.478 Fit side-chains REVERT: A 158 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.8784 (p) REVERT: D 101 LYS cc_start: 0.6128 (pptt) cc_final: 0.5225 (tmtt) REVERT: E 101 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.8588 (mptt) REVERT: F 22 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8725 (t0) REVERT: F 101 LYS cc_start: 0.6096 (mptt) cc_final: 0.5694 (mptt) REVERT: F 289 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8659 (mm-30) REVERT: G 281 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8399 (mm-30) REVERT: G 289 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8021 (tm-30) outliers start: 25 outliers final: 15 residues processed: 133 average time/residue: 0.5971 time to fit residues: 87.8905 Evaluate side-chains 131 residues out of total 1841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 289 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 24 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 15 optimal weight: 0.0870 chunk 174 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 overall best weight: 6.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.052074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.042435 restraints weight = 52729.026| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 2.99 r_work: 0.2485 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2375 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17465 Z= 0.159 Angle : 0.515 12.676 23604 Z= 0.279 Chirality : 0.041 0.157 2681 Planarity : 0.003 0.050 3080 Dihedral : 5.235 87.518 2397 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.22 % Favored : 95.37 % Rotamer: Outliers : 1.47 % Allowed : 24.66 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.17), residues: 2205 helix: 2.29 (0.26), residues: 403 sheet: 0.39 (0.20), residues: 594 loop : -0.87 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 233 TYR 0.012 0.001 TYR B 111 PHE 0.008 0.001 PHE B 76 TRP 0.006 0.001 TRP G 50 HIS 0.003 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00367 (17465) covalent geometry : angle 0.51532 (23604) hydrogen bonds : bond 0.04884 ( 560) hydrogen bonds : angle 5.00023 ( 1506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7018.47 seconds wall clock time: 119 minutes 53.30 seconds (7193.30 seconds total)