Starting phenix.real_space_refine on Fri Sep 19 11:58:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ztc_14957/09_2025/7ztc_14957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ztc_14957/09_2025/7ztc_14957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ztc_14957/09_2025/7ztc_14957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ztc_14957/09_2025/7ztc_14957.map" model { file = "/net/cci-nas-00/data/ceres_data/7ztc_14957/09_2025/7ztc_14957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ztc_14957/09_2025/7ztc_14957.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 168 5.16 5 C 16100 2.51 5 N 4396 2.21 5 O 4972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25652 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "E" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "F" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "G" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "H" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "W" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "X" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "Y" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "Z" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.55, per 1000 atoms: 0.22 Number of scatterers: 25652 At special positions: 0 Unit cell: (97, 101.85, 285.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 16 15.00 O 4972 8.00 N 4396 7.00 C 16100 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: 1.99 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 48 sheets defined 66.2% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.558A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 59' Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.585A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.156A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.965A 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 182 through 194 removed outlier: 3.790A pdb=" N TYR A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.527A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.680A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 4.024A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.585A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.612A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 59' Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.603A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.162A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.515A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.846A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.604A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.310A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.668A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.021A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.645A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.575A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 59' Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.603A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.145A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.865A 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 182 through 194 removed outlier: 3.839A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.526A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.299A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.721A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.020A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.638A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.627A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 55 through 59' Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.597A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.197A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.504A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.866A 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 182 through 194 removed outlier: 3.852A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.549A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.669A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 4.066A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.619A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.614A pdb=" N GLN E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 55 through 59' Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.569A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.179A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.857A 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 182 through 194 removed outlier: 3.847A pdb=" N TYR E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 216 removed outlier: 3.516A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.341A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.684A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 4.095A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 removed outlier: 3.575A pdb=" N GLU E 364 " --> pdb=" O GLN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'F' and resid 55 through 59 removed outlier: 3.645A pdb=" N GLN F 59 " --> pdb=" O GLY F 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 55 through 59' Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.589A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.196A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.836A 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 182 through 194 removed outlier: 3.779A pdb=" N TYR F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 216 removed outlier: 4.161A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 289 through 294 Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.674A pdb=" N LYS F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 4.066A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 removed outlier: 3.612A pdb=" N GLU F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 371 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.654A pdb=" N GLN G 59 " --> pdb=" O GLY G 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 55 through 59' Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.558A pdb=" N MET G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.203A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 removed outlier: 3.871A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 182 through 194 removed outlier: 3.854A pdb=" N TYR G 188 " --> pdb=" O ASP G 184 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 216 removed outlier: 3.536A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 257 through 262 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 283 Processing helix chain 'G' and resid 289 through 294 Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 removed outlier: 3.639A pdb=" N LYS G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 350 through 355 removed outlier: 4.034A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 removed outlier: 3.590A pdb=" N GLU G 364 " --> pdb=" O GLN G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 371 Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.670A pdb=" N GLN H 59 " --> pdb=" O GLY H 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 55 through 59' Processing helix chain 'H' and resid 78 through 92 removed outlier: 3.611A pdb=" N MET H 82 " --> pdb=" O ASN H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 4.182A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 172 through 175 removed outlier: 3.843A pdb=" N ILE H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 172 through 175' Processing helix chain 'H' and resid 182 through 194 removed outlier: 3.796A pdb=" N TYR H 188 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 216 removed outlier: 3.561A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'H' and resid 257 through 262 Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 283 Processing helix chain 'H' and resid 289 through 294 Processing helix chain 'H' and resid 301 through 306 removed outlier: 4.326A pdb=" N TYR H 306 " --> pdb=" O THR H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.671A pdb=" N LYS H 315 " --> pdb=" O ASP H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 350 through 355 removed outlier: 4.042A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 removed outlier: 3.566A pdb=" N GLU H 364 " --> pdb=" O GLN H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 371 Processing helix chain 'W' and resid 2 through 135 Processing helix chain 'X' and resid 2 through 134 Processing helix chain 'Y' and resid 2 through 133 Processing helix chain 'Z' and resid 2 through 134 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.970A pdb=" N THR A 106 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 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 169 through 170 removed outlier: 3.589A pdb=" N LEU A 176 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.611A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) 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 31 removed outlier: 3.606A pdb=" N LYS B 18 " --> pdb=" O ASP B 11 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 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 169 through 170 removed outlier: 3.599A pdb=" N LEU B 176 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.592A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) 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 31 removed outlier: 3.963A pdb=" N THR C 106 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 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 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.573A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) 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 31 removed outlier: 3.532A pdb=" N LYS D 18 " --> pdb=" O ASP D 11 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 107 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 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 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.574A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) 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 31 removed outlier: 3.959A pdb=" N THR E 106 " --> pdb=" O VAL E 10 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 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 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.576A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) 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 31 removed outlier: 4.061A pdb=" N THR F 106 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 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 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.670A pdb=" N THR F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.527A pdb=" N LYS G 18 " --> pdb=" O ASP G 11 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR G 106 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.648A pdb=" N THR G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.522A pdb=" N LYS H 18 " --> pdb=" O ASP H 11 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR H 106 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AF2, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.739A pdb=" N THR H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 238 through 241 removed outlier: 3.623A pdb=" N LYS H 238 " --> pdb=" O ILE H 250 " (cutoff:3.500A) 1595 hydrogen bonds defined for protein. 4170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8434 1.34 - 1.46: 3156 1.46 - 1.57: 14250 1.57 - 1.69: 24 1.69 - 1.81: 296 Bond restraints: 26160 Sorted by residual: bond pdb=" CD1 TYR C 169 " pdb=" CE1 TYR C 169 " ideal model delta sigma weight residual 1.382 1.338 0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CD1 TYR H 169 " pdb=" CE1 TYR H 169 " ideal model delta sigma weight residual 1.382 1.341 0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CD1 TYR F 169 " pdb=" CE1 TYR F 169 " ideal model delta sigma weight residual 1.382 1.341 0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CB TYR C 169 " pdb=" CG TYR C 169 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.20e-02 2.07e+03 1.80e+00 bond pdb=" CB THR C 160 " pdb=" CG2 THR C 160 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 ... (remaining 26155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 34829 2.47 - 4.94: 694 4.94 - 7.41: 67 7.41 - 9.88: 13 9.88 - 12.35: 5 Bond angle restraints: 35608 Sorted by residual: angle pdb=" CA TYR F 169 " pdb=" CB TYR F 169 " pdb=" CG TYR F 169 " ideal model delta sigma weight residual 113.90 104.27 9.63 1.80e+00 3.09e-01 2.86e+01 angle pdb=" N GLY D 42 " pdb=" CA GLY D 42 " pdb=" C GLY D 42 " ideal model delta sigma weight residual 113.18 125.53 -12.35 2.37e+00 1.78e-01 2.72e+01 angle pdb=" N GLY E 42 " pdb=" CA GLY E 42 " pdb=" C GLY E 42 " ideal model delta sigma weight residual 113.18 125.00 -11.82 2.37e+00 1.78e-01 2.49e+01 angle pdb=" N GLY F 42 " pdb=" CA GLY F 42 " pdb=" C GLY F 42 " ideal model delta sigma weight residual 113.18 124.90 -11.72 2.37e+00 1.78e-01 2.45e+01 angle pdb=" CA TYR E 169 " pdb=" CB TYR E 169 " pdb=" CG TYR E 169 " ideal model delta sigma weight residual 113.90 105.66 8.24 1.80e+00 3.09e-01 2.09e+01 ... (remaining 35603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.80: 15414 32.80 - 65.60: 268 65.60 - 98.40: 32 98.40 - 131.19: 8 131.19 - 163.99: 6 Dihedral angle restraints: 15728 sinusoidal: 5688 harmonic: 10040 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.99 -163.99 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.41 -163.41 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O2A ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PA ADP H 401 " pdb=" PB ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.19 -163.19 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 15725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2844 0.046 - 0.093: 894 0.093 - 0.139: 313 0.139 - 0.185: 22 0.185 - 0.231: 11 Chirality restraints: 4084 Sorted by residual: chirality pdb=" CA GLN B 49 " pdb=" N GLN B 49 " pdb=" C GLN B 49 " pdb=" CB GLN B 49 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PHE C 124 " pdb=" N PHE C 124 " pdb=" C PHE C 124 " pdb=" CB PHE C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE E 124 " pdb=" N PHE E 124 " pdb=" C PHE E 124 " pdb=" CB PHE E 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 4081 not shown) Planarity restraints: 4600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 169 " 0.044 2.00e-02 2.50e+03 2.80e-02 1.56e+01 pdb=" CG TYR F 169 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR F 169 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR F 169 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 169 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR F 169 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR F 169 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 169 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 169 " 0.038 2.00e-02 2.50e+03 2.70e-02 1.46e+01 pdb=" CG TYR E 169 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR E 169 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR E 169 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 169 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 169 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR E 169 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 169 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 166 " 0.008 2.00e-02 2.50e+03 2.69e-02 1.45e+01 pdb=" CG TYR A 166 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 166 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 166 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 166 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 166 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 166 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR A 166 " -0.037 2.00e-02 2.50e+03 ... (remaining 4597 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 337 2.68 - 3.23: 25786 3.23 - 3.79: 38478 3.79 - 4.34: 50792 4.34 - 4.90: 84354 Nonbonded interactions: 199747 Sorted by model distance: nonbonded pdb=" OG1 THR C 160 " pdb=" O LEU C 178 " model vdw 2.123 3.040 nonbonded pdb=" OG1 THR G 160 " pdb=" O LEU G 178 " model vdw 2.133 3.040 nonbonded pdb=" OG1 THR D 160 " pdb=" O LEU D 178 " model vdw 2.133 3.040 nonbonded pdb=" OG1 THR B 160 " pdb=" O LEU B 178 " model vdw 2.147 3.040 nonbonded pdb=" OG1 THR F 160 " pdb=" O LEU F 178 " model vdw 2.148 3.040 ... (remaining 199742 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' selection = chain 'H' } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.640 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26160 Z= 0.167 Angle : 0.845 12.349 35608 Z= 0.441 Chirality : 0.050 0.231 4084 Planarity : 0.010 0.124 4600 Dihedral : 13.851 163.992 9256 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.20 (0.14), residues: 2904 helix: -2.50 (0.12), residues: 1096 sheet: -0.67 (0.23), residues: 496 loop : -0.59 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.004 ARG B 147 TYR 0.064 0.006 TYR E 169 PHE 0.017 0.001 PHE E 124 TRP 0.033 0.003 TRP D 356 HIS 0.009 0.002 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00359 (26160) covalent geometry : angle 0.84479 (35608) hydrogen bonds : bond 0.18872 ( 1579) hydrogen bonds : angle 6.86707 ( 4170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.8866 (mmp) cc_final: 0.8613 (mmp) REVERT: C 44 MET cc_start: 0.7984 (tpt) cc_final: 0.7214 (ttp) REVERT: C 75 ILE cc_start: 0.8704 (mt) cc_final: 0.8246 (tt) REVERT: C 208 ILE cc_start: 0.9168 (mm) cc_final: 0.8947 (mt) REVERT: D 44 MET cc_start: 0.8187 (tpt) cc_final: 0.7246 (ttt) REVERT: D 305 MET cc_start: 0.8378 (mmm) cc_final: 0.7958 (mmt) REVERT: E 9 VAL cc_start: 0.8998 (t) cc_final: 0.8726 (m) REVERT: E 44 MET cc_start: 0.8287 (tpt) cc_final: 0.7866 (tpt) REVERT: E 205 GLU cc_start: 0.7820 (tt0) cc_final: 0.7479 (tt0) REVERT: E 360 GLN cc_start: 0.8240 (mm110) cc_final: 0.7823 (tp40) REVERT: F 24 ASP cc_start: 0.7170 (t0) cc_final: 0.6907 (m-30) REVERT: F 25 ASP cc_start: 0.8104 (t70) cc_final: 0.7526 (t0) REVERT: F 44 MET cc_start: 0.8163 (tpt) cc_final: 0.7813 (tpt) REVERT: F 205 GLU cc_start: 0.7953 (tt0) cc_final: 0.7671 (mt-10) REVERT: F 313 MET cc_start: 0.8887 (tpp) cc_final: 0.8637 (ttp) REVERT: G 43 VAL cc_start: 0.9032 (m) cc_final: 0.8774 (p) REVERT: G 65 LEU cc_start: 0.8918 (mp) cc_final: 0.8632 (mp) REVERT: G 92 ASN cc_start: 0.8140 (t0) cc_final: 0.7864 (m-40) REVERT: H 129 THR cc_start: 0.8152 (p) cc_final: 0.7666 (p) REVERT: H 201 THR cc_start: 0.8361 (m) cc_final: 0.8117 (t) REVERT: H 272 CYS cc_start: 0.7644 (m) cc_final: 0.7236 (m) outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.1617 time to fit residues: 154.9932 Evaluate side-chains 290 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS A 88 HIS A 252 ASN B 87 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 252 ASN C 49 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS C 354 GLN D 87 HIS D 88 HIS D 246 GLN E 87 HIS E 252 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 HIS F 246 GLN G 87 HIS G 88 HIS H 87 HIS H 88 HIS ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.076518 restraints weight = 58547.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.078607 restraints weight = 32141.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.080029 restraints weight = 20749.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.080956 restraints weight = 14953.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.081633 restraints weight = 11752.454| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 26160 Z= 0.221 Angle : 0.753 9.204 35608 Z= 0.371 Chirality : 0.048 0.254 4084 Planarity : 0.005 0.055 4600 Dihedral : 9.715 150.827 3792 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.27 % Allowed : 8.50 % Favored : 89.24 % 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: -0.76 (0.15), residues: 2904 helix: -0.54 (0.15), residues: 1064 sheet: -0.11 (0.23), residues: 496 loop : -0.45 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 206 TYR 0.069 0.002 TYR F 169 PHE 0.032 0.002 PHE C 124 TRP 0.022 0.003 TRP D 356 HIS 0.008 0.002 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00510 (26160) covalent geometry : angle 0.75269 (35608) hydrogen bonds : bond 0.04533 ( 1579) hydrogen bonds : angle 4.86636 ( 4170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8596 (mmm) cc_final: 0.8237 (mmm) REVERT: A 123 MET cc_start: 0.8619 (tpp) cc_final: 0.8259 (tpp) REVERT: A 157 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: A 283 MET cc_start: 0.8830 (mmp) cc_final: 0.8305 (mmm) REVERT: B 123 MET cc_start: 0.8784 (tpp) cc_final: 0.8285 (tpp) REVERT: B 169 TYR cc_start: 0.8376 (m-80) cc_final: 0.8154 (m-80) REVERT: B 288 ASP cc_start: 0.7668 (p0) cc_final: 0.7334 (t0) REVERT: C 82 MET cc_start: 0.8398 (mmm) cc_final: 0.7971 (tpt) REVERT: C 250 ILE cc_start: 0.8166 (mt) cc_final: 0.7945 (pt) REVERT: D 44 MET cc_start: 0.8342 (tpt) cc_final: 0.7569 (ttt) REVERT: D 82 MET cc_start: 0.8394 (mmm) cc_final: 0.8085 (tmm) REVERT: D 205 GLU cc_start: 0.7667 (tt0) cc_final: 0.7234 (pt0) REVERT: D 305 MET cc_start: 0.8354 (mmm) cc_final: 0.7996 (mmt) REVERT: D 325 MET cc_start: 0.8051 (mmt) cc_final: 0.7641 (tpt) REVERT: E 44 MET cc_start: 0.8432 (tpt) cc_final: 0.7901 (tpt) REVERT: E 272 CYS cc_start: 0.7009 (m) cc_final: 0.6736 (m) REVERT: E 355 MET cc_start: 0.8210 (mtp) cc_final: 0.7955 (mtt) REVERT: F 24 ASP cc_start: 0.6993 (t0) cc_final: 0.6769 (m-30) REVERT: F 25 ASP cc_start: 0.8144 (t70) cc_final: 0.7458 (t0) REVERT: F 72 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6899 (pp20) REVERT: F 205 GLU cc_start: 0.8154 (tt0) cc_final: 0.7925 (mt-10) REVERT: F 313 MET cc_start: 0.8981 (tpp) cc_final: 0.8616 (ttt) REVERT: G 115 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8842 (t0) REVERT: G 123 MET cc_start: 0.8264 (tpp) cc_final: 0.8004 (tpt) REVERT: G 300 SER cc_start: 0.8427 (t) cc_final: 0.7990 (m) REVERT: H 123 MET cc_start: 0.8771 (tpp) cc_final: 0.8491 (tpp) REVERT: H 169 TYR cc_start: 0.6926 (m-80) cc_final: 0.6627 (m-80) outliers start: 56 outliers final: 29 residues processed: 339 average time/residue: 0.1366 time to fit residues: 78.1696 Evaluate side-chains 259 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 212 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 140 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 322 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 115 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS E 252 ASN F 49 GLN ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.075520 restraints weight = 58667.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.077477 restraints weight = 33150.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.078832 restraints weight = 21768.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.079754 restraints weight = 15840.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.080338 restraints weight = 12482.453| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26160 Z= 0.198 Angle : 0.687 8.949 35608 Z= 0.334 Chirality : 0.046 0.231 4084 Planarity : 0.005 0.051 4600 Dihedral : 8.903 143.209 3792 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.59 % Allowed : 10.64 % Favored : 86.77 % 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: -0.40 (0.15), residues: 2904 helix: 0.03 (0.16), residues: 1064 sheet: -0.01 (0.22), residues: 496 loop : -0.47 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 116 TYR 0.032 0.002 TYR H 169 PHE 0.028 0.002 PHE F 124 TRP 0.016 0.002 TRP C 79 HIS 0.006 0.001 HIS F 371 Details of bonding type rmsd covalent geometry : bond 0.00457 (26160) covalent geometry : angle 0.68726 (35608) hydrogen bonds : bond 0.04413 ( 1579) hydrogen bonds : angle 4.55055 ( 4170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 246 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8618 (mmm) cc_final: 0.8238 (mmm) REVERT: A 123 MET cc_start: 0.8737 (tpp) cc_final: 0.8407 (tpp) REVERT: A 157 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: A 283 MET cc_start: 0.8818 (mmp) cc_final: 0.8547 (mmp) REVERT: B 283 MET cc_start: 0.9151 (mmt) cc_final: 0.8760 (mmt) REVERT: B 288 ASP cc_start: 0.7572 (p0) cc_final: 0.7331 (t0) REVERT: C 82 MET cc_start: 0.8548 (mmm) cc_final: 0.8190 (tpt) REVERT: C 155 SER cc_start: 0.8754 (t) cc_final: 0.8380 (t) REVERT: C 340 TRP cc_start: 0.8815 (t60) cc_final: 0.8227 (t60) REVERT: D 305 MET cc_start: 0.8323 (mmm) cc_final: 0.7995 (mmt) REVERT: E 44 MET cc_start: 0.8468 (tpt) cc_final: 0.7979 (tpt) REVERT: F 25 ASP cc_start: 0.8034 (t70) cc_final: 0.7793 (t0) REVERT: F 205 GLU cc_start: 0.8140 (tt0) cc_final: 0.7865 (mt-10) REVERT: F 313 MET cc_start: 0.9005 (tpp) cc_final: 0.8502 (ttt) REVERT: G 92 ASN cc_start: 0.8559 (t0) cc_final: 0.7798 (m-40) REVERT: G 300 SER cc_start: 0.8407 (t) cc_final: 0.7993 (m) REVERT: H 123 MET cc_start: 0.8847 (tpp) cc_final: 0.8601 (tpp) REVERT: H 305 MET cc_start: 0.7857 (mmt) cc_final: 0.7599 (mmt) outliers start: 64 outliers final: 36 residues processed: 292 average time/residue: 0.1312 time to fit residues: 65.7691 Evaluate side-chains 260 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 29 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 72 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 334 optimal weight: 30.0000 chunk 261 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 273 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 111 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN E 353 GLN F 49 GLN G 115 ASN ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.098453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.076679 restraints weight = 57973.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.078782 restraints weight = 31913.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.080203 restraints weight = 20595.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.081149 restraints weight = 14856.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.081835 restraints weight = 11602.332| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26160 Z= 0.140 Angle : 0.626 9.062 35608 Z= 0.298 Chirality : 0.044 0.203 4084 Planarity : 0.004 0.052 4600 Dihedral : 8.344 163.405 3792 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.51 % Allowed : 11.77 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.02 (0.16), residues: 2904 helix: 0.73 (0.17), residues: 1016 sheet: 0.06 (0.21), residues: 496 loop : -0.45 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 116 TYR 0.030 0.001 TYR H 169 PHE 0.023 0.001 PHE F 124 TRP 0.011 0.001 TRP C 79 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00310 (26160) covalent geometry : angle 0.62635 (35608) hydrogen bonds : bond 0.03875 ( 1579) hydrogen bonds : angle 4.27082 ( 4170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 253 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8286 (t0) cc_final: 0.8035 (t0) REVERT: A 82 MET cc_start: 0.8695 (mmm) cc_final: 0.8374 (mmm) REVERT: A 123 MET cc_start: 0.8682 (tpp) cc_final: 0.8453 (tpp) REVERT: A 157 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: A 283 MET cc_start: 0.8829 (mmp) cc_final: 0.8562 (mmp) REVERT: B 291 LYS cc_start: 0.8389 (tttp) cc_final: 0.7599 (mptt) REVERT: C 82 MET cc_start: 0.8595 (mmm) cc_final: 0.8158 (tpt) REVERT: C 117 GLU cc_start: 0.7631 (tt0) cc_final: 0.7192 (tm-30) REVERT: C 155 SER cc_start: 0.8770 (t) cc_final: 0.8451 (t) REVERT: C 340 TRP cc_start: 0.8658 (t60) cc_final: 0.7890 (t60) REVERT: D 305 MET cc_start: 0.8284 (mmm) cc_final: 0.7960 (mmt) REVERT: E 311 ASP cc_start: 0.8105 (t0) cc_final: 0.7860 (t0) REVERT: E 355 MET cc_start: 0.8047 (mtp) cc_final: 0.7761 (mtt) REVERT: F 25 ASP cc_start: 0.7887 (t70) cc_final: 0.7232 (t0) REVERT: F 205 GLU cc_start: 0.8115 (tt0) cc_final: 0.7910 (mt-10) REVERT: G 92 ASN cc_start: 0.8589 (t0) cc_final: 0.7813 (m-40) REVERT: G 115 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8620 (t0) REVERT: G 132 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6635 (tpp) REVERT: G 300 SER cc_start: 0.8515 (t) cc_final: 0.8055 (m) REVERT: H 82 MET cc_start: 0.8315 (mmm) cc_final: 0.7964 (tmm) REVERT: H 123 MET cc_start: 0.8834 (tpp) cc_final: 0.8596 (tpp) outliers start: 62 outliers final: 37 residues processed: 296 average time/residue: 0.1318 time to fit residues: 66.7109 Evaluate side-chains 270 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 282 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 92 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 309 optimal weight: 30.0000 chunk 260 optimal weight: 4.9990 chunk 301 optimal weight: 30.0000 chunk 263 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 334 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN G 115 ASN ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.097248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.075517 restraints weight = 58349.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.077579 restraints weight = 32047.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.078985 restraints weight = 20759.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.079924 restraints weight = 14986.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.080594 restraints weight = 11748.209| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26160 Z= 0.167 Angle : 0.640 9.441 35608 Z= 0.308 Chirality : 0.044 0.207 4084 Planarity : 0.004 0.052 4600 Dihedral : 8.095 176.037 3792 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.03 % Allowed : 12.62 % Favored : 84.34 % 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 (0.16), residues: 2904 helix: 0.87 (0.17), residues: 1016 sheet: 0.08 (0.21), residues: 496 loop : -0.56 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 290 TYR 0.025 0.001 TYR B 362 PHE 0.024 0.001 PHE C 124 TRP 0.013 0.001 TRP C 79 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00380 (26160) covalent geometry : angle 0.63983 (35608) hydrogen bonds : bond 0.03952 ( 1579) hydrogen bonds : angle 4.26038 ( 4170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 232 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8545 (t0) cc_final: 0.8300 (t0) REVERT: A 82 MET cc_start: 0.8720 (mmm) cc_final: 0.8495 (mmm) REVERT: A 123 MET cc_start: 0.8694 (tpp) cc_final: 0.8470 (tpp) REVERT: A 283 MET cc_start: 0.8803 (mmp) cc_final: 0.8534 (mmp) REVERT: B 291 LYS cc_start: 0.8431 (tttp) cc_final: 0.7649 (mptt) REVERT: C 82 MET cc_start: 0.8721 (mmm) cc_final: 0.8253 (tpt) REVERT: C 117 GLU cc_start: 0.7532 (tt0) cc_final: 0.7189 (tm-30) REVERT: C 340 TRP cc_start: 0.8691 (t60) cc_final: 0.8004 (t60) REVERT: D 305 MET cc_start: 0.8299 (mmm) cc_final: 0.7958 (mmt) REVERT: E 311 ASP cc_start: 0.8170 (t0) cc_final: 0.7934 (t0) REVERT: E 355 MET cc_start: 0.8057 (mtp) cc_final: 0.7766 (mtt) REVERT: F 25 ASP cc_start: 0.7458 (t70) cc_final: 0.7236 (t0) REVERT: G 92 ASN cc_start: 0.8576 (t0) cc_final: 0.7708 (m-40) REVERT: G 132 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.6633 (tpp) REVERT: G 300 SER cc_start: 0.8558 (t) cc_final: 0.8143 (m) REVERT: G 337 TYR cc_start: 0.8063 (m-80) cc_final: 0.7849 (m-80) REVERT: H 123 MET cc_start: 0.8844 (tpp) cc_final: 0.8511 (tpp) outliers start: 75 outliers final: 51 residues processed: 284 average time/residue: 0.1333 time to fit residues: 65.0562 Evaluate side-chains 268 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 282 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 245 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 301 optimal weight: 30.0000 chunk 203 optimal weight: 0.9980 chunk 294 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 chunk 176 optimal weight: 8.9990 chunk 297 optimal weight: 20.0000 chunk 210 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN D 49 GLN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 HIS G 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.098927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.077139 restraints weight = 58032.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.079237 restraints weight = 31813.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.080661 restraints weight = 20493.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.081629 restraints weight = 14734.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.082313 restraints weight = 11499.249| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26160 Z= 0.129 Angle : 0.603 10.746 35608 Z= 0.284 Chirality : 0.043 0.189 4084 Planarity : 0.004 0.051 4600 Dihedral : 7.373 155.330 3792 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.47 % Allowed : 13.71 % Favored : 83.82 % 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: 0.22 (0.16), residues: 2904 helix: 1.11 (0.17), residues: 1016 sheet: 0.06 (0.21), residues: 496 loop : -0.48 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.022 0.001 TYR F 169 PHE 0.017 0.001 PHE F 124 TRP 0.009 0.001 TRP E 356 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00285 (26160) covalent geometry : angle 0.60305 (35608) hydrogen bonds : bond 0.03597 ( 1579) hydrogen bonds : angle 4.06583 ( 4170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 245 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8398 (t0) cc_final: 0.8126 (t0) REVERT: A 123 MET cc_start: 0.8583 (tpp) cc_final: 0.8302 (tpp) REVERT: A 283 MET cc_start: 0.8770 (mmp) cc_final: 0.8533 (mmp) REVERT: B 216 LEU cc_start: 0.8996 (tp) cc_final: 0.8538 (tp) REVERT: B 291 LYS cc_start: 0.8325 (tttp) cc_final: 0.7618 (mptt) REVERT: C 12 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8378 (p0) REVERT: C 117 GLU cc_start: 0.7642 (tt0) cc_final: 0.7274 (tm-30) REVERT: C 340 TRP cc_start: 0.8577 (t60) cc_final: 0.7731 (t60) REVERT: D 305 MET cc_start: 0.8286 (mmm) cc_final: 0.7923 (mmt) REVERT: E 47 MET cc_start: 0.3593 (mmm) cc_final: 0.3361 (tpt) REVERT: E 311 ASP cc_start: 0.8190 (t0) cc_final: 0.7876 (t0) REVERT: E 355 MET cc_start: 0.7971 (mtp) cc_final: 0.7721 (mtt) REVERT: F 25 ASP cc_start: 0.7412 (t70) cc_final: 0.7169 (t0) REVERT: G 92 ASN cc_start: 0.8501 (t0) cc_final: 0.7724 (m-40) REVERT: G 300 SER cc_start: 0.8501 (t) cc_final: 0.8125 (m) REVERT: G 337 TYR cc_start: 0.7894 (m-80) cc_final: 0.7687 (m-80) REVERT: H 82 MET cc_start: 0.8287 (mmm) cc_final: 0.7751 (tmm) REVERT: H 123 MET cc_start: 0.8776 (tpp) cc_final: 0.8475 (tpp) REVERT: H 269 MET cc_start: 0.7226 (mtm) cc_final: 0.6744 (ptp) REVERT: H 283 MET cc_start: 0.8313 (tpp) cc_final: 0.7312 (mpp) outliers start: 61 outliers final: 43 residues processed: 290 average time/residue: 0.1345 time to fit residues: 66.3923 Evaluate side-chains 267 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 282 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 97 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 210 optimal weight: 0.0770 chunk 245 optimal weight: 0.8980 chunk 267 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 241 optimal weight: 0.8980 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.097332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.075710 restraints weight = 58507.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.077708 restraints weight = 32682.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.079048 restraints weight = 21346.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.079994 restraints weight = 15571.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.080638 restraints weight = 12247.693| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26160 Z= 0.154 Angle : 0.636 11.179 35608 Z= 0.302 Chirality : 0.044 0.237 4084 Planarity : 0.004 0.050 4600 Dihedral : 7.067 139.560 3792 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.83 % Allowed : 14.12 % Favored : 83.05 % 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: 0.22 (0.16), residues: 2904 helix: 1.15 (0.17), residues: 1016 sheet: 0.05 (0.21), residues: 496 loop : -0.51 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 290 TYR 0.020 0.001 TYR B 362 PHE 0.045 0.002 PHE A 124 TRP 0.011 0.001 TRP C 79 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00352 (26160) covalent geometry : angle 0.63593 (35608) hydrogen bonds : bond 0.03763 ( 1579) hydrogen bonds : angle 4.12542 ( 4170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 230 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8436 (t0) cc_final: 0.8169 (t0) REVERT: A 283 MET cc_start: 0.8774 (mmp) cc_final: 0.8513 (mmp) REVERT: B 47 MET cc_start: 0.5290 (tpp) cc_final: 0.4878 (tpt) REVERT: B 216 LEU cc_start: 0.8985 (tp) cc_final: 0.8596 (tp) REVERT: B 291 LYS cc_start: 0.8375 (tttp) cc_final: 0.7659 (mptt) REVERT: C 12 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8328 (p0) REVERT: C 117 GLU cc_start: 0.7629 (tt0) cc_final: 0.7225 (tm-30) REVERT: C 340 TRP cc_start: 0.8645 (t60) cc_final: 0.7927 (t60) REVERT: D 305 MET cc_start: 0.8259 (mmm) cc_final: 0.7934 (mmt) REVERT: E 355 MET cc_start: 0.7873 (mtp) cc_final: 0.7595 (mtt) REVERT: F 25 ASP cc_start: 0.7392 (t70) cc_final: 0.7191 (t0) REVERT: G 92 ASN cc_start: 0.8511 (t0) cc_final: 0.7699 (m-40) REVERT: G 300 SER cc_start: 0.8571 (t) cc_final: 0.8219 (m) REVERT: H 82 MET cc_start: 0.8523 (mmm) cc_final: 0.8032 (tmm) REVERT: H 123 MET cc_start: 0.8793 (tpp) cc_final: 0.8414 (tpp) REVERT: H 283 MET cc_start: 0.8369 (tpp) cc_final: 0.7243 (mpp) outliers start: 70 outliers final: 55 residues processed: 282 average time/residue: 0.1362 time to fit residues: 66.1270 Evaluate side-chains 276 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 220 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 282 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 221 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 309 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 295 optimal weight: 20.0000 chunk 242 optimal weight: 4.9990 chunk 292 optimal weight: 30.0000 chunk 132 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 ASN ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.075292 restraints weight = 58308.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.077370 restraints weight = 32053.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.078755 restraints weight = 20663.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.079666 restraints weight = 14940.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.080350 restraints weight = 11789.791| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26160 Z= 0.157 Angle : 0.643 11.997 35608 Z= 0.304 Chirality : 0.044 0.231 4084 Planarity : 0.004 0.049 4600 Dihedral : 6.788 125.865 3792 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.63 % Allowed : 14.44 % Favored : 82.93 % 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: 0.23 (0.16), residues: 2904 helix: 1.24 (0.17), residues: 1008 sheet: 0.01 (0.21), residues: 496 loop : -0.55 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 95 TYR 0.017 0.001 TYR B 362 PHE 0.036 0.001 PHE F 124 TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00361 (26160) covalent geometry : angle 0.64256 (35608) hydrogen bonds : bond 0.03718 ( 1579) hydrogen bonds : angle 4.12619 ( 4170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8429 (t0) cc_final: 0.8138 (t0) REVERT: A 123 MET cc_start: 0.8305 (tpp) cc_final: 0.8072 (tpp) REVERT: A 157 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: A 266 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.9160 (m-10) REVERT: A 283 MET cc_start: 0.8746 (mmp) cc_final: 0.8523 (mmp) REVERT: B 47 MET cc_start: 0.5489 (tpp) cc_final: 0.5123 (tpt) REVERT: B 216 LEU cc_start: 0.9035 (tp) cc_final: 0.8627 (tp) REVERT: B 291 LYS cc_start: 0.8403 (tttp) cc_final: 0.7669 (mptt) REVERT: C 12 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8238 (p0) REVERT: C 340 TRP cc_start: 0.8653 (t60) cc_final: 0.7884 (t60) REVERT: D 305 MET cc_start: 0.8239 (mmm) cc_final: 0.7903 (mmt) REVERT: E 355 MET cc_start: 0.7899 (mtp) cc_final: 0.7641 (mtt) REVERT: F 25 ASP cc_start: 0.7438 (t70) cc_final: 0.7214 (t0) REVERT: F 82 MET cc_start: 0.9053 (tpt) cc_final: 0.8767 (tpp) REVERT: G 283 MET cc_start: 0.8564 (mmp) cc_final: 0.8224 (mmp) REVERT: G 300 SER cc_start: 0.8488 (t) cc_final: 0.8144 (m) REVERT: H 82 MET cc_start: 0.8568 (mmm) cc_final: 0.8159 (tmm) REVERT: H 283 MET cc_start: 0.8378 (tpp) cc_final: 0.7200 (mpp) outliers start: 65 outliers final: 51 residues processed: 275 average time/residue: 0.1319 time to fit residues: 62.4016 Evaluate side-chains 268 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 124 PHE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 282 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 133 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 327 optimal weight: 30.0000 chunk 3 optimal weight: 0.0370 chunk 188 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 293 optimal weight: 20.0000 chunk 204 optimal weight: 0.6980 chunk 268 optimal weight: 0.6980 chunk 319 optimal weight: 30.0000 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 HIS H 252 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.100687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.078831 restraints weight = 57998.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.080957 restraints weight = 31744.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.082410 restraints weight = 20388.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.083383 restraints weight = 14617.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084033 restraints weight = 11404.692| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26160 Z= 0.114 Angle : 0.599 11.195 35608 Z= 0.280 Chirality : 0.042 0.184 4084 Planarity : 0.004 0.049 4600 Dihedral : 6.213 109.258 3792 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.62 % Allowed : 15.45 % Favored : 82.93 % 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: 0.42 (0.16), residues: 2904 helix: 1.42 (0.17), residues: 1008 sheet: 0.04 (0.21), residues: 496 loop : -0.42 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.019 0.001 TYR F 169 PHE 0.045 0.001 PHE F 124 TRP 0.010 0.001 TRP A 86 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00245 (26160) covalent geometry : angle 0.59920 (35608) hydrogen bonds : bond 0.03241 ( 1579) hydrogen bonds : angle 3.90074 ( 4170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8192 (t0) cc_final: 0.7952 (t0) REVERT: A 283 MET cc_start: 0.8742 (mmp) cc_final: 0.8541 (mmp) REVERT: B 47 MET cc_start: 0.5580 (tpp) cc_final: 0.5198 (tpt) REVERT: B 216 LEU cc_start: 0.9014 (tp) cc_final: 0.8561 (tp) REVERT: B 291 LYS cc_start: 0.8151 (tttp) cc_final: 0.7547 (mptt) REVERT: C 123 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8560 (mmm) REVERT: C 340 TRP cc_start: 0.8527 (t60) cc_final: 0.7585 (t60) REVERT: E 44 MET cc_start: 0.8742 (mmm) cc_final: 0.8348 (tpt) REVERT: E 132 MET cc_start: 0.8398 (ppp) cc_final: 0.7548 (pmm) REVERT: E 355 MET cc_start: 0.7801 (mtp) cc_final: 0.7560 (mtt) REVERT: F 82 MET cc_start: 0.9048 (tpt) cc_final: 0.8773 (tpp) REVERT: G 82 MET cc_start: 0.9206 (tpt) cc_final: 0.8966 (tpp) REVERT: G 92 ASN cc_start: 0.8687 (t0) cc_final: 0.7782 (m-40) REVERT: G 283 MET cc_start: 0.8515 (mmp) cc_final: 0.8189 (mmp) REVERT: G 300 SER cc_start: 0.8401 (t) cc_final: 0.8103 (m) REVERT: H 82 MET cc_start: 0.8394 (mmm) cc_final: 0.8119 (tmm) REVERT: H 283 MET cc_start: 0.8347 (tpp) cc_final: 0.7102 (mpp) outliers start: 40 outliers final: 27 residues processed: 280 average time/residue: 0.1372 time to fit residues: 66.2529 Evaluate side-chains 255 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 252 ASN Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 205 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 329 optimal weight: 40.0000 chunk 142 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 226 optimal weight: 0.8980 chunk 73 optimal weight: 0.0170 chunk 110 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.078787 restraints weight = 57697.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.080931 restraints weight = 31549.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.082384 restraints weight = 20205.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.083378 restraints weight = 14476.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.084066 restraints weight = 11238.733| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26160 Z= 0.118 Angle : 0.614 11.926 35608 Z= 0.288 Chirality : 0.042 0.227 4084 Planarity : 0.004 0.050 4600 Dihedral : 6.037 102.511 3792 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.38 % Allowed : 15.98 % Favored : 82.65 % 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: 0.51 (0.16), residues: 2904 helix: 1.49 (0.17), residues: 1008 sheet: 0.15 (0.21), residues: 496 loop : -0.38 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.020 0.001 TYR F 169 PHE 0.042 0.001 PHE F 124 TRP 0.012 0.001 TRP E 86 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00256 (26160) covalent geometry : angle 0.61363 (35608) hydrogen bonds : bond 0.03258 ( 1579) hydrogen bonds : angle 3.87535 ( 4170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8203 (t0) cc_final: 0.7994 (t0) REVERT: B 47 MET cc_start: 0.5577 (tpp) cc_final: 0.5197 (tpt) REVERT: B 123 MET cc_start: 0.8561 (tpp) cc_final: 0.8276 (tpp) REVERT: B 216 LEU cc_start: 0.9005 (tp) cc_final: 0.8559 (tp) REVERT: B 291 LYS cc_start: 0.8117 (tttp) cc_final: 0.7472 (mttt) REVERT: C 340 TRP cc_start: 0.8534 (t60) cc_final: 0.7598 (t60) REVERT: E 132 MET cc_start: 0.8681 (ppp) cc_final: 0.7393 (pmm) REVERT: E 355 MET cc_start: 0.7731 (mtp) cc_final: 0.7479 (mtt) REVERT: G 12 ASN cc_start: 0.8626 (t0) cc_final: 0.7948 (p0) REVERT: G 82 MET cc_start: 0.9202 (tpt) cc_final: 0.8062 (tmm) REVERT: G 300 SER cc_start: 0.8364 (t) cc_final: 0.8140 (m) REVERT: H 82 MET cc_start: 0.8396 (mmm) cc_final: 0.8127 (tmm) REVERT: H 283 MET cc_start: 0.8359 (tpp) cc_final: 0.7103 (mpp) outliers start: 34 outliers final: 29 residues processed: 263 average time/residue: 0.1321 time to fit residues: 59.3206 Evaluate side-chains 259 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 252 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 40.0000 chunk 322 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 167 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.099858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.078091 restraints weight = 57786.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.080211 restraints weight = 31603.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.081660 restraints weight = 20312.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.082646 restraints weight = 14566.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083155 restraints weight = 11337.048| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26160 Z= 0.127 Angle : 0.610 10.122 35608 Z= 0.288 Chirality : 0.043 0.231 4084 Planarity : 0.004 0.049 4600 Dihedral : 5.940 98.546 3792 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.50 % Allowed : 15.94 % Favored : 82.56 % 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: 0.61 (0.16), residues: 2904 helix: 1.50 (0.17), residues: 1008 sheet: 0.17 (0.20), residues: 544 loop : -0.27 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.029 0.001 TYR B 362 PHE 0.041 0.001 PHE F 124 TRP 0.010 0.001 TRP D 356 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00283 (26160) covalent geometry : angle 0.61050 (35608) hydrogen bonds : bond 0.03286 ( 1579) hydrogen bonds : angle 3.89937 ( 4170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3411.16 seconds wall clock time: 59 minutes 57.20 seconds (3597.20 seconds total)