Starting phenix.real_space_refine on Sun Jun 22 08:11:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ztc_14957/06_2025/7ztc_14957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ztc_14957/06_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_14957/06_2025/7ztc_14957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ztc_14957/06_2025/7ztc_14957.map" model { file = "/net/cci-nas-00/data/ceres_data/7ztc_14957/06_2025/7ztc_14957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ztc_14957/06_2025/7ztc_14957.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.70, per 1000 atoms: 0.57 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: 6.41 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.71 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: 9.84 Time building geometry restraints manager: 7.59 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 56.070 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.150 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.033 0.003 TRP D 356 HIS 0.009 0.002 HIS G 87 PHE 0.017 0.001 PHE E 124 TYR 0.064 0.006 TYR E 169 ARG 0.027 0.004 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.18872 ( 1579) hydrogen bonds : angle 6.86707 ( 4170) covalent geometry : bond 0.00359 (26160) covalent geometry : angle 0.84479 (35608) *********************** 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 : 2.850 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: 0.7213 (ttp) REVERT: C 75 ILE cc_start: 0.8704 (mt) cc_final: 0.8254 (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: 0.7245 (ttt) REVERT: D 305 MET cc_start: 0.8378 (mmm) cc_final: 0.7957 (mmt) REVERT: E 9 VAL cc_start: 0.8998 (t) cc_final: 0.8723 (m) REVERT: E 44 MET cc_start: 0.8287 (tpt) cc_final: 0.7862 (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: 0.7822 (tp40) REVERT: F 24 ASP cc_start: 0.7170 (t0) cc_final: 0.6906 (m-30) REVERT: F 25 ASP cc_start: 0.8104 (t70) cc_final: 0.7527 (t0) REVERT: F 44 MET cc_start: 0.8163 (tpt) cc_final: 0.7808 (tpt) REVERT: F 205 GLU cc_start: 0.7953 (tt0) cc_final: 0.7658 (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: 0.8777 (p) REVERT: G 65 LEU cc_start: 0.8918 (mp) cc_final: 0.8631 (mp) REVERT: G 92 ASN cc_start: 0.8140 (t0) cc_final: 0.7865 (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: 0.8116 (t) REVERT: H 272 CYS cc_start: 0.7644 (m) cc_final: 0.7238 (m) outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.3633 time to fit residues: 348.1091 Evaluate side-chains 289 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 10.0000 chunk 257 optimal weight: 0.4980 chunk 142 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 266 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 308 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 87 HIS A 88 HIS A 252 ASN B 87 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN C 49 GLN C 88 HIS C 101 HIS ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN D 87 HIS D 88 HIS D 246 GLN E 87 HIS E 101 HIS E 252 ASN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 HIS ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 87 HIS G 88 HIS H 87 HIS H 88 HIS H 173 HIS ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.102404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.080711 restraints weight = 57505.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082868 restraints weight = 31346.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.084304 restraints weight = 20145.045| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26160 Z= 0.153 Angle : 0.680 8.317 35608 Z= 0.331 Chirality : 0.045 0.223 4084 Planarity : 0.004 0.040 4600 Dihedral : 9.590 149.003 3792 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.98 % Allowed : 8.21 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 2904 helix: -0.46 (0.15), residues: 1104 sheet: 0.02 (0.23), residues: 496 loop : -0.21 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 356 HIS 0.006 0.001 HIS B 87 PHE 0.034 0.002 PHE C 124 TYR 0.056 0.002 TYR F 169 ARG 0.005 0.000 ARG E 183 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 1579) hydrogen bonds : angle 4.74034 ( 4170) covalent geometry : bond 0.00337 (26160) covalent geometry : angle 0.67985 (35608) *********************** 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 371 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 322 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8566 (mmm) cc_final: 0.8275 (mmm) REVERT: A 123 MET cc_start: 0.8680 (tpp) cc_final: 0.8253 (tpp) REVERT: A 283 MET cc_start: 0.8834 (mmp) cc_final: 0.8431 (mmm) REVERT: B 123 MET cc_start: 0.8757 (tpp) cc_final: 0.8246 (tpp) REVERT: B 169 TYR cc_start: 0.8293 (m-80) cc_final: 0.8057 (m-80) REVERT: B 283 MET cc_start: 0.9202 (mmt) cc_final: 0.8832 (mmt) REVERT: B 288 ASP cc_start: 0.7638 (p0) cc_final: 0.7280 (t0) REVERT: C 82 MET cc_start: 0.8163 (mmm) cc_final: 0.7859 (tpp) REVERT: C 227 MET cc_start: 0.8494 (mmm) cc_final: 0.8289 (mmt) REVERT: C 250 ILE cc_start: 0.8126 (mt) cc_final: 0.7887 (pt) REVERT: D 44 MET cc_start: 0.8345 (tpt) cc_final: 0.7666 (ttt) REVERT: D 82 MET cc_start: 0.8234 (mmm) cc_final: 0.8009 (tmm) REVERT: D 205 GLU cc_start: 0.7579 (tt0) cc_final: 0.7066 (pt0) REVERT: D 305 MET cc_start: 0.8244 (mmm) cc_final: 0.7949 (mmt) REVERT: E 44 MET cc_start: 0.8434 (tpt) cc_final: 0.8123 (tpt) REVERT: E 205 GLU cc_start: 0.8145 (tt0) cc_final: 0.7573 (tt0) REVERT: E 355 MET cc_start: 0.8177 (mtp) cc_final: 0.7912 (mtt) REVERT: E 360 GLN cc_start: 0.8097 (mm110) cc_final: 0.7831 (tp40) REVERT: F 25 ASP cc_start: 0.8169 (t70) cc_final: 0.7544 (t0) REVERT: F 82 MET cc_start: 0.8783 (tpp) cc_final: 0.8357 (mmm) REVERT: F 205 GLU cc_start: 0.8092 (tt0) cc_final: 0.7778 (mt-10) REVERT: F 313 MET cc_start: 0.8872 (tpp) cc_final: 0.8573 (ttt) REVERT: G 82 MET cc_start: 0.8729 (mmm) cc_final: 0.8072 (mmm) REVERT: G 92 ASN cc_start: 0.8444 (t0) cc_final: 0.7786 (m-40) REVERT: G 115 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8526 (t0) REVERT: G 253 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7823 (mt-10) REVERT: G 300 SER cc_start: 0.8230 (t) cc_final: 0.7806 (m) REVERT: H 123 MET cc_start: 0.8678 (tpp) cc_final: 0.8334 (tpp) REVERT: H 270 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7288 (mt-10) outliers start: 49 outliers final: 23 residues processed: 356 average time/residue: 0.3141 time to fit residues: 186.9476 Evaluate side-chains 263 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 278 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 106 THR Chi-restraints excluded: chain F residue 129 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 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 G residue 311 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 267 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 338 optimal weight: 40.0000 chunk 77 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 288 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 292 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS B 115 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN E 252 ASN F 49 GLN F 101 HIS G 40 HIS ** 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 = 0.3286 r_free = 0.3286 target = 0.093741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.072169 restraints weight = 59394.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.074151 restraints weight = 33451.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.075488 restraints weight = 21911.435| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 26160 Z= 0.352 Angle : 0.845 10.226 35608 Z= 0.421 Chirality : 0.052 0.276 4084 Planarity : 0.006 0.058 4600 Dihedral : 9.345 143.425 3792 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.16 % Allowed : 10.36 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 2904 helix: -0.35 (0.16), residues: 1056 sheet: -0.10 (0.22), residues: 496 loop : -0.72 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 79 HIS 0.009 0.002 HIS C 275 PHE 0.032 0.002 PHE C 124 TYR 0.042 0.003 TYR H 169 ARG 0.005 0.001 ARG E 335 Details of bonding type rmsd hydrogen bonds : bond 0.05270 ( 1579) hydrogen bonds : angle 5.00565 ( 4170) covalent geometry : bond 0.00827 (26160) covalent geometry : angle 0.84550 (35608) *********************** 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 312 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 234 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8685 (mmm) cc_final: 0.8384 (mmm) REVERT: B 288 ASP cc_start: 0.7662 (p0) cc_final: 0.7352 (t0) REVERT: D 305 MET cc_start: 0.8399 (mmm) cc_final: 0.8106 (mmt) REVERT: E 283 MET cc_start: 0.8870 (tpp) cc_final: 0.8650 (tpp) REVERT: E 355 MET cc_start: 0.8321 (mtp) cc_final: 0.8047 (mtt) REVERT: F 25 ASP cc_start: 0.7734 (t70) cc_final: 0.7493 (t0) REVERT: F 169 TYR cc_start: 0.6602 (m-10) cc_final: 0.6391 (m-10) REVERT: F 205 GLU cc_start: 0.8152 (tt0) cc_final: 0.7939 (mt-10) REVERT: F 313 MET cc_start: 0.9158 (tpp) cc_final: 0.8687 (ttt) REVERT: F 325 MET cc_start: 0.7917 (mmp) cc_final: 0.7599 (mmm) REVERT: G 113 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8289 (mmmm) REVERT: G 300 SER cc_start: 0.8599 (t) cc_final: 0.8152 (m) REVERT: H 123 MET cc_start: 0.8808 (tpp) cc_final: 0.8550 (tpp) outliers start: 78 outliers final: 53 residues processed: 298 average time/residue: 0.2937 time to fit residues: 148.7353 Evaluate side-chains 257 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 2.549 ------------------------------------------------------------------------------- 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 338 SER 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 157 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 361 GLU 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 122 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 190 MET 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 57 GLU Chi-restraints excluded: chain E residue 64 ILE 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 49 GLN 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 F residue 282 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 57 GLU 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 113 LYS 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 G residue 303 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 201 THR 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 84 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 313 optimal weight: 40.0000 chunk 339 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 335 optimal weight: 30.0000 chunk 146 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 88 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN D 12 ASN D 59 GLN E 252 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.097954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.076000 restraints weight = 58581.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.078092 restraints weight = 32214.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.079509 restraints weight = 20831.748| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26160 Z= 0.148 Angle : 0.643 9.591 35608 Z= 0.309 Chirality : 0.044 0.212 4084 Planarity : 0.004 0.053 4600 Dihedral : 8.481 159.293 3792 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.55 % Allowed : 12.14 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 2904 helix: 0.56 (0.17), residues: 1008 sheet: -0.05 (0.21), residues: 496 loop : -0.56 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 86 HIS 0.005 0.001 HIS G 371 PHE 0.029 0.001 PHE C 124 TYR 0.018 0.001 TYR H 169 ARG 0.003 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 1579) hydrogen bonds : angle 4.37599 ( 4170) covalent geometry : bond 0.00332 (26160) covalent geometry : angle 0.64339 (35608) *********************** 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 313 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 250 time to evaluate : 2.549 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8641 (t0) REVERT: A 78 ASN cc_start: 0.8550 (t0) cc_final: 0.8291 (t0) REVERT: A 82 MET cc_start: 0.8683 (mmm) cc_final: 0.8277 (mmm) REVERT: A 157 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: A 272 CYS cc_start: 0.8047 (p) cc_final: 0.7793 (p) REVERT: B 289 ILE cc_start: 0.9337 (mm) cc_final: 0.9136 (mm) REVERT: B 291 LYS cc_start: 0.8479 (tttp) cc_final: 0.7519 (mttt) REVERT: C 44 MET cc_start: 0.8018 (tpp) cc_final: 0.7755 (tpp) REVERT: C 117 GLU cc_start: 0.7688 (tt0) cc_final: 0.7178 (tm-30) REVERT: C 155 SER cc_start: 0.8861 (t) cc_final: 0.8546 (t) REVERT: C 340 TRP cc_start: 0.8701 (t60) cc_final: 0.7990 (t60) REVERT: D 305 MET cc_start: 0.8330 (mmm) cc_final: 0.8005 (mmt) REVERT: E 123 MET cc_start: 0.8683 (tpp) cc_final: 0.8480 (tpp) REVERT: E 246 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8239 (mt0) REVERT: E 283 MET cc_start: 0.8667 (tpp) cc_final: 0.8436 (tpp) REVERT: E 355 MET cc_start: 0.8251 (mtp) cc_final: 0.7942 (mtt) REVERT: F 205 GLU cc_start: 0.8061 (tt0) cc_final: 0.7825 (mt-10) REVERT: F 313 MET cc_start: 0.8968 (tpp) cc_final: 0.8425 (ttt) REVERT: G 92 ASN cc_start: 0.8631 (t0) cc_final: 0.7746 (m-40) REVERT: G 300 SER cc_start: 0.8440 (t) cc_final: 0.8022 (m) REVERT: H 82 MET cc_start: 0.8448 (mmm) cc_final: 0.7996 (tmm) REVERT: H 123 MET cc_start: 0.8843 (tpp) cc_final: 0.8614 (tpp) outliers start: 63 outliers final: 39 residues processed: 301 average time/residue: 0.3071 time to fit residues: 157.2350 Evaluate side-chains 266 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain C residue 43 VAL 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 D residue 160 THR Chi-restraints excluded: chain D residue 216 LEU 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 64 ILE 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 140 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 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 43 VAL 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 65 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 201 THR 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 93 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 338 optimal weight: 40.0000 chunk 331 optimal weight: 30.0000 chunk 92 optimal weight: 0.1980 chunk 168 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 335 optimal weight: 30.0000 chunk 146 optimal weight: 0.0770 chunk 245 optimal weight: 2.9990 overall best weight: 1.4542 ------------------------------------------------------------------------------- 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN E 252 ASN ** G 371 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 = 0.3362 r_free = 0.3362 target = 0.098053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.076219 restraints weight = 58402.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.078324 restraints weight = 31805.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.079751 restraints weight = 20447.707| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4195 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= 0.145 Angle : 0.627 9.432 35608 Z= 0.300 Chirality : 0.044 0.211 4084 Planarity : 0.004 0.054 4600 Dihedral : 8.096 179.529 3792 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.14 % Allowed : 13.55 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2904 helix: 0.89 (0.18), residues: 960 sheet: 0.01 (0.21), residues: 496 loop : -0.47 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.006 0.001 HIS G 371 PHE 0.026 0.001 PHE C 124 TYR 0.033 0.001 TYR H 169 ARG 0.007 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 1579) hydrogen bonds : angle 4.21220 ( 4170) covalent geometry : bond 0.00325 (26160) covalent geometry : angle 0.62702 (35608) *********************** 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 296 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 2.792 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8910 (t0) cc_final: 0.8653 (t0) REVERT: A 78 ASN cc_start: 0.8430 (t0) cc_final: 0.8146 (t0) REVERT: A 82 MET cc_start: 0.8662 (mmm) cc_final: 0.8358 (mmm) REVERT: A 123 MET cc_start: 0.8758 (tpp) cc_final: 0.8370 (tpp) REVERT: A 272 CYS cc_start: 0.8062 (p) cc_final: 0.7832 (p) REVERT: A 305 MET cc_start: 0.8298 (mmm) cc_final: 0.8047 (mtp) REVERT: B 291 LYS cc_start: 0.8363 (tttp) cc_final: 0.7619 (mptt) REVERT: C 44 MET cc_start: 0.7994 (tpp) cc_final: 0.7745 (tpp) REVERT: C 340 TRP cc_start: 0.8642 (t60) cc_final: 0.7900 (t60) REVERT: D 305 MET cc_start: 0.8304 (mmm) cc_final: 0.7971 (mmt) REVERT: E 44 MET cc_start: 0.8613 (tpt) cc_final: 0.8257 (tpt) REVERT: E 283 MET cc_start: 0.8624 (tpp) cc_final: 0.8368 (tpp) REVERT: E 355 MET cc_start: 0.8200 (mtp) cc_final: 0.7887 (mtt) REVERT: F 313 MET cc_start: 0.8949 (tpp) cc_final: 0.8511 (mtp) REVERT: G 92 ASN cc_start: 0.8635 (t0) cc_final: 0.7711 (m-40) REVERT: G 113 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8120 (mmmm) REVERT: G 300 SER cc_start: 0.8509 (t) cc_final: 0.8119 (m) REVERT: H 123 MET cc_start: 0.8844 (tpp) cc_final: 0.8564 (tpp) outliers start: 53 outliers final: 40 residues processed: 284 average time/residue: 0.3012 time to fit residues: 146.0510 Evaluate side-chains 260 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 338 SER 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 247 VAL Chi-restraints excluded: chain C residue 43 VAL 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 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 160 THR 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 64 ILE 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 140 LEU 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 106 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 113 LYS 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 H residue 65 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 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 76 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 313 optimal weight: 40.0000 chunk 236 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 309 optimal weight: 30.0000 chunk 316 optimal weight: 30.0000 chunk 256 optimal weight: 9.9990 chunk 329 optimal weight: 30.0000 chunk 195 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN E 252 ASN F 161 HIS ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.092436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.070695 restraints weight = 59416.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.072666 restraints weight = 33133.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.074024 restraints weight = 21685.792| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 26160 Z= 0.329 Angle : 0.808 11.768 35608 Z= 0.399 Chirality : 0.051 0.281 4084 Planarity : 0.006 0.056 4600 Dihedral : 8.371 179.858 3792 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.07 % Allowed : 14.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 2904 helix: 0.44 (0.17), residues: 952 sheet: -0.24 (0.21), residues: 496 loop : -0.95 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 79 HIS 0.010 0.002 HIS G 371 PHE 0.033 0.002 PHE F 124 TYR 0.023 0.002 TYR C 169 ARG 0.007 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 1579) hydrogen bonds : angle 4.79054 ( 4170) covalent geometry : bond 0.00775 (26160) covalent geometry : angle 0.80756 (35608) *********************** 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 284 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 208 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8733 (t0) cc_final: 0.8347 (t0) REVERT: A 82 MET cc_start: 0.8607 (mmm) cc_final: 0.8277 (mmm) REVERT: B 356 TRP cc_start: 0.8816 (OUTLIER) cc_final: 0.7996 (m-90) REVERT: D 305 MET cc_start: 0.8300 (mmm) cc_final: 0.7994 (mmt) REVERT: E 205 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8454 (tt0) REVERT: E 246 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8359 (mt0) REVERT: E 283 MET cc_start: 0.8799 (tpp) cc_final: 0.8358 (mpp) REVERT: E 355 MET cc_start: 0.8229 (mtp) cc_final: 0.7958 (mtt) REVERT: F 313 MET cc_start: 0.9162 (tpp) cc_final: 0.8650 (ttt) REVERT: G 113 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8357 (mmmm) REVERT: G 300 SER cc_start: 0.8705 (t) cc_final: 0.8213 (m) REVERT: H 82 MET cc_start: 0.8692 (mmm) cc_final: 0.8102 (tmm) REVERT: H 123 MET cc_start: 0.8726 (tpp) cc_final: 0.8349 (tpp) REVERT: H 269 MET cc_start: 0.7558 (mtm) cc_final: 0.7065 (ptp) outliers start: 76 outliers final: 57 residues processed: 271 average time/residue: 0.3399 time to fit residues: 158.5273 Evaluate side-chains 257 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 338 SER 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 162 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 356 TRP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 351 THR 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 274 ILE 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 64 ILE 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 E residue 370 VAL 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 162 THR Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 179 ASP 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 G residue 351 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 212 ILE 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 214 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 91 optimal weight: 0.0970 chunk 249 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 339 optimal weight: 30.0000 chunk 31 optimal weight: 0.8980 chunk 327 optimal weight: 30.0000 chunk 23 optimal weight: 1.9990 chunk 319 optimal weight: 30.0000 chunk 111 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN C 252 ASN D 101 HIS ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** G 371 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 = 0.3359 r_free = 0.3359 target = 0.097834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.076174 restraints weight = 58378.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.078222 restraints weight = 32350.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.079618 restraints weight = 20971.552| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26160 Z= 0.124 Angle : 0.616 11.192 35608 Z= 0.292 Chirality : 0.043 0.209 4084 Planarity : 0.004 0.052 4600 Dihedral : 7.461 177.513 3792 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.86 % Allowed : 15.01 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2904 helix: 0.79 (0.17), residues: 1000 sheet: -0.27 (0.21), residues: 504 loop : -0.59 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.004 0.001 HIS G 371 PHE 0.033 0.001 PHE F 124 TYR 0.014 0.001 TYR G 143 ARG 0.002 0.000 ARG D 62 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 1579) hydrogen bonds : angle 4.14931 ( 4170) covalent geometry : bond 0.00269 (26160) covalent geometry : angle 0.61626 (35608) *********************** 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 286 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 2.731 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6443 (mm-40) REVERT: A 78 ASN cc_start: 0.8347 (t0) cc_final: 0.8047 (t0) REVERT: A 82 MET cc_start: 0.8644 (mmm) cc_final: 0.8435 (mmm) REVERT: B 132 MET cc_start: 0.7737 (ttp) cc_final: 0.7505 (ttp) REVERT: B 291 LYS cc_start: 0.8312 (tttp) cc_final: 0.7581 (mptt) REVERT: C 340 TRP cc_start: 0.8581 (t60) cc_final: 0.7813 (t60) REVERT: D 107 GLU cc_start: 0.7932 (tt0) cc_final: 0.7727 (tt0) REVERT: D 305 MET cc_start: 0.8211 (mmm) cc_final: 0.7856 (mmt) REVERT: E 205 GLU cc_start: 0.8687 (tt0) cc_final: 0.8458 (tt0) REVERT: E 246 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: E 355 MET cc_start: 0.8164 (mtp) cc_final: 0.7894 (mtt) REVERT: F 313 MET cc_start: 0.8938 (tpp) cc_final: 0.8510 (mtp) REVERT: G 113 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8098 (mmmm) REVERT: G 115 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8596 (t0) REVERT: G 283 MET cc_start: 0.8608 (mmp) cc_final: 0.8271 (mmp) REVERT: G 300 SER cc_start: 0.8445 (t) cc_final: 0.8022 (m) REVERT: H 82 MET cc_start: 0.8402 (mmm) cc_final: 0.8069 (tmm) REVERT: H 269 MET cc_start: 0.7282 (mtm) cc_final: 0.7020 (ptp) outliers start: 46 outliers final: 34 residues processed: 275 average time/residue: 0.3206 time to fit residues: 149.2517 Evaluate side-chains 255 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 64 ILE 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 140 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 272 CYS 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 G residue 106 THR Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 115 ASN 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 292 ASP Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain H residue 65 LEU 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 272 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 215 optimal weight: 0.0870 chunk 114 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 87 optimal weight: 0.0870 chunk 279 optimal weight: 4.9990 chunk 286 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 309 optimal weight: 30.0000 chunk 208 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN G 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.100339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.078722 restraints weight = 58186.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.080792 restraints weight = 32304.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082199 restraints weight = 20882.585| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26160 Z= 0.115 Angle : 0.600 11.458 35608 Z= 0.282 Chirality : 0.042 0.210 4084 Planarity : 0.004 0.051 4600 Dihedral : 6.625 134.526 3792 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.66 % Allowed : 15.66 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2904 helix: 1.19 (0.17), residues: 992 sheet: -0.05 (0.21), residues: 496 loop : -0.50 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.005 0.001 HIS G 371 PHE 0.044 0.001 PHE A 124 TYR 0.024 0.001 TYR F 169 ARG 0.007 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 1579) hydrogen bonds : angle 3.94977 ( 4170) covalent geometry : bond 0.00247 (26160) covalent geometry : angle 0.60027 (35608) *********************** 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 297 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 2.779 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8335 (t0) cc_final: 0.8052 (t0) REVERT: A 123 MET cc_start: 0.8605 (tpp) cc_final: 0.8253 (tpp) REVERT: B 291 LYS cc_start: 0.8094 (tttp) cc_final: 0.7470 (mttt) REVERT: C 340 TRP cc_start: 0.8544 (t60) cc_final: 0.7666 (t60) REVERT: D 305 MET cc_start: 0.8123 (mmm) cc_final: 0.7674 (mmt) REVERT: E 246 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: E 355 MET cc_start: 0.8091 (mtp) cc_final: 0.7802 (mtt) REVERT: F 313 MET cc_start: 0.8889 (tpp) cc_final: 0.8405 (mtp) REVERT: G 132 MET cc_start: 0.8317 (tmm) cc_final: 0.8097 (tmm) REVERT: G 283 MET cc_start: 0.8518 (mmp) cc_final: 0.8164 (mmp) REVERT: G 300 SER cc_start: 0.8401 (t) cc_final: 0.8113 (m) REVERT: G 305 MET cc_start: 0.7798 (mtp) cc_final: 0.7576 (mtp) REVERT: H 283 MET cc_start: 0.8421 (tpp) cc_final: 0.7157 (mpp) outliers start: 41 outliers final: 27 residues processed: 286 average time/residue: 0.3093 time to fit residues: 150.5573 Evaluate side-chains 249 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 351 THR 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 E residue 64 ILE 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 E residue 272 CYS 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 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 65 LEU 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 272 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 13 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 265 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 306 optimal weight: 40.0000 chunk 130 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 161 HIS ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN C 354 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.096472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.074456 restraints weight = 58748.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.076529 restraints weight = 32346.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.077849 restraints weight = 20946.177| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26160 Z= 0.178 Angle : 0.674 11.777 35608 Z= 0.322 Chirality : 0.045 0.251 4084 Planarity : 0.005 0.052 4600 Dihedral : 6.851 132.184 3792 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.66 % Allowed : 16.30 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2904 helix: 1.27 (0.18), residues: 952 sheet: -0.15 (0.21), residues: 504 loop : -0.55 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 86 HIS 0.006 0.001 HIS G 371 PHE 0.059 0.002 PHE D 352 TYR 0.021 0.002 TYR E 362 ARG 0.007 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 1579) hydrogen bonds : angle 4.13100 ( 4170) covalent geometry : bond 0.00413 (26160) covalent geometry : angle 0.67404 (35608) *********************** 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 261 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 2.605 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8408 (t0) cc_final: 0.8145 (t0) REVERT: A 123 MET cc_start: 0.8576 (tpp) cc_final: 0.8029 (tmm) REVERT: B 47 MET cc_start: 0.5306 (tpp) cc_final: 0.4595 (tpt) REVERT: B 291 LYS cc_start: 0.8449 (tttp) cc_final: 0.7643 (mptt) REVERT: C 340 TRP cc_start: 0.8694 (t60) cc_final: 0.8043 (t60) REVERT: D 305 MET cc_start: 0.8226 (mmm) cc_final: 0.7838 (mmt) REVERT: E 246 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: E 355 MET cc_start: 0.8137 (mtp) cc_final: 0.7887 (mtt) REVERT: F 153 MET cc_start: 0.8014 (ttm) cc_final: 0.7799 (ttt) REVERT: F 313 MET cc_start: 0.9085 (tpp) cc_final: 0.8652 (ttt) REVERT: G 300 SER cc_start: 0.8603 (t) cc_final: 0.8243 (m) REVERT: H 82 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.6634 (tmm) outliers start: 41 outliers final: 33 residues processed: 253 average time/residue: 0.3008 time to fit residues: 130.1294 Evaluate side-chains 249 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 64 ILE 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 E residue 272 CYS 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 162 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 292 ASP Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 106 THR 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 272 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 283 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 314 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.095420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.073480 restraints weight = 58519.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.075525 restraints weight = 32225.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.076834 restraints weight = 20841.594| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4869 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 : 0.695 12.193 35608 Z= 0.333 Chirality : 0.046 0.252 4084 Planarity : 0.005 0.051 4600 Dihedral : 6.885 129.054 3792 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.74 % Allowed : 16.38 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2904 helix: 1.10 (0.18), residues: 952 sheet: -0.21 (0.21), residues: 504 loop : -0.65 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 86 HIS 0.006 0.001 HIS C 275 PHE 0.055 0.002 PHE D 352 TYR 0.036 0.002 TYR H 169 ARG 0.007 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 1579) hydrogen bonds : angle 4.26612 ( 4170) covalent geometry : bond 0.00462 (26160) covalent geometry : angle 0.69475 (35608) ********************** 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 258 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 2.953 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8413 (t0) cc_final: 0.8129 (t0) REVERT: B 47 MET cc_start: 0.5254 (tpp) cc_final: 0.4534 (tpt) REVERT: C 340 TRP cc_start: 0.8757 (t60) cc_final: 0.8157 (t60) REVERT: D 305 MET cc_start: 0.8266 (mmm) cc_final: 0.7910 (mmt) REVERT: E 246 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: E 355 MET cc_start: 0.8130 (mtp) cc_final: 0.7873 (mtt) REVERT: F 313 MET cc_start: 0.9132 (tpp) cc_final: 0.8617 (ttt) REVERT: G 113 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8450 (mmmm) REVERT: G 300 SER cc_start: 0.8637 (t) cc_final: 0.8179 (p) outliers start: 43 outliers final: 34 residues processed: 248 average time/residue: 0.3100 time to fit residues: 131.1333 Evaluate side-chains 243 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 64 ILE 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 282 ILE 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 G residue 113 LYS Chi-restraints excluded: chain G residue 129 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 292 ASP Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain H residue 65 LEU 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 272 CYS Chi-restraints excluded: chain H residue 313 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 105 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 266 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 264 optimal weight: 7.9990 chunk 313 optimal weight: 40.0000 chunk 17 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 chunk 330 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.071393 restraints weight = 59508.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.073278 restraints weight = 33815.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.074575 restraints weight = 22358.588| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 26160 Z= 0.315 Angle : 0.803 13.956 35608 Z= 0.391 Chirality : 0.050 0.276 4084 Planarity : 0.005 0.050 4600 Dihedral : 7.371 141.939 3792 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.94 % Allowed : 16.14 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 2904 helix: 0.71 (0.17), residues: 952 sheet: -0.28 (0.21), residues: 496 loop : -0.99 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.009 0.001 HIS C 275 PHE 0.049 0.002 PHE D 352 TYR 0.045 0.002 TYR H 169 ARG 0.007 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 1579) hydrogen bonds : angle 4.64457 ( 4170) covalent geometry : bond 0.00739 (26160) covalent geometry : angle 0.80318 (35608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6825.78 seconds wall clock time: 119 minutes 54.14 seconds (7194.14 seconds total)