Starting phenix.real_space_refine on Thu Feb 5 14:44:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ku3_62573/02_2026/9ku3_62573.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ku3_62573/02_2026/9ku3_62573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ku3_62573/02_2026/9ku3_62573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ku3_62573/02_2026/9ku3_62573.map" model { file = "/net/cci-nas-00/data/ceres_data/9ku3_62573/02_2026/9ku3_62573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ku3_62573/02_2026/9ku3_62573.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 11324 2.51 5 N 3023 2.21 5 O 3374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17769 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2922 Classifications: {'peptide': 379} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain breaks: 2 Chain: "B" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2961 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 18, 'TRANS': 365} Chain breaks: 2 Chain: "C" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2913 Classifications: {'peptide': 378} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 358} Chain breaks: 2 Chain: "D" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2943 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 18, 'TRANS': 363} Chain breaks: 2 Chain: "E" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2922 Classifications: {'peptide': 379} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain breaks: 2 Chain: "F" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2943 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 18, 'TRANS': 363} Chain breaks: 2 Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'UNK:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'UNK:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'UNK:plan-1': 3} Unresolved non-hydrogen planarities: 3 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N GLY A 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 261 " occ=0.00 residue: pdb=" N GLY A 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 281 " occ=0.00 residue: pdb=" N GLY B 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 261 " occ=0.00 residue: pdb=" N GLY B 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 281 " occ=0.00 residue: pdb=" N GLY C 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY C 261 " occ=0.00 residue: pdb=" N GLY C 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY C 281 " occ=0.00 residue: pdb=" N GLY D 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 261 " occ=0.00 residue: pdb=" N GLY D 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 281 " occ=0.00 residue: pdb=" N GLY E 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY E 261 " occ=0.00 residue: pdb=" N GLY E 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY E 281 " occ=0.00 residue: pdb=" N GLY F 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY F 261 " occ=0.00 residue: pdb=" N GLY F 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY F 281 " occ=0.00 Time building chain proxies: 3.71, per 1000 atoms: 0.21 Number of scatterers: 17769 At special positions: 0 Unit cell: (159.16, 157.32, 86.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 3374 8.00 N 3023 7.00 C 11324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 705.6 milliseconds 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4280 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 33 sheets defined 35.3% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 47 through 60 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.621A pdb=" N THR A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 128 through 134 removed outlier: 3.574A pdb=" N GLY A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 419 through 426 removed outlier: 3.724A pdb=" N ASP A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP A 426 " --> pdb=" O MET A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 447 removed outlier: 3.589A pdb=" N LYS A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 61 removed outlier: 3.999A pdb=" N VAL B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 58 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 90 through 103 removed outlier: 5.104A pdb=" N GLU B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 128 through 134 Processing helix chain 'B' and resid 148 through 152 removed outlier: 4.005A pdb=" N MET B 152 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 removed outlier: 4.608A pdb=" N ALA B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.655A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.581A pdb=" N VAL B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 426 through 447 removed outlier: 3.509A pdb=" N LEU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 61 removed outlier: 3.564A pdb=" N TYR C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 83 removed outlier: 3.623A pdb=" N ASP C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 128 through 134 removed outlier: 3.554A pdb=" N LYS C 132 " --> pdb=" O THR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 217 through 228 removed outlier: 3.558A pdb=" N GLY C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 255 Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 381 through 385 Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 426 through 447 removed outlier: 3.543A pdb=" N LYS C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 61 removed outlier: 3.846A pdb=" N LYS D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 90 through 103 removed outlier: 3.675A pdb=" N LYS D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU D 96 " --> pdb=" O LYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 128 through 134 Processing helix chain 'D' and resid 153 through 162 removed outlier: 3.853A pdb=" N ALA D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASN D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 228 Processing helix chain 'D' and resid 246 through 255 removed outlier: 3.718A pdb=" N ALA D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 382 through 387 removed outlier: 3.544A pdb=" N HIS D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 419 through 425 removed outlier: 3.727A pdb=" N ASP D 425 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 446 removed outlier: 3.643A pdb=" N LEU D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET D 446 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 66 through 83 removed outlier: 3.803A pdb=" N ASP E 83 " --> pdb=" O LEU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 100 Processing helix chain 'E' and resid 128 through 134 Processing helix chain 'E' and resid 153 through 162 Processing helix chain 'E' and resid 217 through 228 Processing helix chain 'E' and resid 246 through 255 removed outlier: 3.659A pdb=" N ALA E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 312 Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 419 through 426 removed outlier: 3.784A pdb=" N ASP E 425 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP E 426 " --> pdb=" O MET E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 447 removed outlier: 3.620A pdb=" N LYS E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 61 removed outlier: 3.869A pdb=" N VAL F 53 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 90 through 103 removed outlier: 3.933A pdb=" N LYS F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU F 96 " --> pdb=" O LYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 128 through 133 Processing helix chain 'F' and resid 153 through 162 removed outlier: 4.317A pdb=" N ALA F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 228 Processing helix chain 'F' and resid 246 through 255 removed outlier: 3.781A pdb=" N ALA F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 413 through 415 No H-bonds generated for 'chain 'F' and resid 413 through 415' Processing helix chain 'F' and resid 419 through 425 Processing helix chain 'F' and resid 426 through 447 removed outlier: 3.623A pdb=" N ILE F 441 " --> pdb=" O LYS F 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 7.029A pdb=" N TYR A 277 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 89 removed outlier: 3.850A pdb=" N GLU A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A 328 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 115 removed outlier: 7.011A pdb=" N THR A 111 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 removed outlier: 6.676A pdb=" N THR A 172 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 144 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN A 170 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 364 through 365 removed outlier: 7.296A pdb=" N ILE A 290 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ILE A 318 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 292 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 235 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU A 293 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A 237 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 211 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL A 418 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS A 200 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.982A pdb=" N TYR B 277 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER B 265 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B 275 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 89 removed outlier: 3.692A pdb=" N GLU B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 328 " --> pdb=" O THR B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107 removed outlier: 4.348A pdb=" N ASP B 189 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 112 removed outlier: 6.897A pdb=" N THR B 111 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 139 through 143 removed outlier: 7.156A pdb=" N THR B 172 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 364 through 365 removed outlier: 7.090A pdb=" N ILE B 290 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE B 318 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 292 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 235 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU B 293 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU B 237 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASP B 238 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL B 418 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS B 200 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 89 removed outlier: 7.104A pdb=" N TYR C 277 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 87 through 89 removed outlier: 7.017A pdb=" N VAL C 328 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 112 through 115 Processing sheet with id=AB6, first strand: chain 'C' and resid 147 through 148 removed outlier: 6.674A pdb=" N THR C 172 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE C 144 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLN C 170 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 364 through 365 removed outlier: 7.217A pdb=" N ILE C 290 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ILE C 318 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL C 292 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 211 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL C 418 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LYS C 200 " --> pdb=" O VAL C 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 87 through 89 removed outlier: 7.091A pdb=" N TYR D 277 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER D 265 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU D 275 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 87 through 89 removed outlier: 6.499A pdb=" N GLU D 338 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL D 328 " --> pdb=" O THR D 344 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 104 through 107 Processing sheet with id=AC2, first strand: chain 'D' and resid 110 through 112 removed outlier: 7.097A pdb=" N THR D 111 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.626A pdb=" N LYS D 143 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 364 through 365 removed outlier: 6.626A pdb=" N ILE D 317 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE D 290 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE D 318 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL D 292 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL D 418 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS D 200 " --> pdb=" O VAL D 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 87 through 89 removed outlier: 7.036A pdb=" N TYR E 277 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 87 through 89 removed outlier: 7.147A pdb=" N GLU E 338 " --> pdb=" O VAL E 334 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL E 328 " --> pdb=" O THR E 344 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 112 through 115 Processing sheet with id=AC8, first strand: chain 'E' and resid 147 through 148 removed outlier: 6.712A pdb=" N THR E 172 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE E 144 " --> pdb=" O GLN E 170 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN E 170 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 364 through 365 removed outlier: 7.242A pdb=" N ILE E 290 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE E 318 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL E 292 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E 211 " --> pdb=" O ASP E 238 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL E 418 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS E 200 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 87 through 89 removed outlier: 3.849A pdb=" N VAL F 264 " --> pdb=" O TYR F 277 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 87 through 89 removed outlier: 6.692A pdb=" N GLU F 338 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL F 328 " --> pdb=" O THR F 344 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 104 through 106 Processing sheet with id=AD4, first strand: chain 'F' and resid 110 through 112 removed outlier: 6.858A pdb=" N THR F 111 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 147 through 148 removed outlier: 5.520A pdb=" N ILE F 141 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL F 174 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 364 through 365 removed outlier: 7.149A pdb=" N ILE F 290 " --> pdb=" O VAL F 316 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE F 318 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL F 292 " --> pdb=" O ILE F 318 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE F 235 " --> pdb=" O ALA F 291 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU F 293 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU F 237 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL F 211 " --> pdb=" O ASP F 238 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL F 418 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS F 200 " --> pdb=" O VAL F 418 " (cutoff:3.500A) 736 hydrogen bonds defined for protein. 2037 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3521 1.33 - 1.45: 3522 1.45 - 1.58: 10882 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 18021 Sorted by residual: bond pdb=" N ILE A 191 " pdb=" CA ILE A 191 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.24e-02 6.50e+03 1.10e+01 bond pdb=" CZ ARG F 49 " pdb=" NH2 ARG F 49 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.83e+00 bond pdb=" N THR D 204 " pdb=" CA THR D 204 " ideal model delta sigma weight residual 1.453 1.482 -0.029 9.20e-03 1.18e+04 9.78e+00 bond pdb=" CZ ARG C 210 " pdb=" NH2 ARG C 210 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.39e+00 bond pdb=" CZ ARG A 240 " pdb=" NH2 ARG A 240 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.36e+00 ... (remaining 18016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 17028 1.88 - 3.76: 6325 3.76 - 5.64: 881 5.64 - 7.51: 44 7.51 - 9.39: 4 Bond angle restraints: 24282 Sorted by residual: angle pdb=" N ILE B 144 " pdb=" CA ILE B 144 " pdb=" C ILE B 144 " ideal model delta sigma weight residual 110.42 104.75 5.67 9.40e-01 1.13e+00 3.64e+01 angle pdb=" N VAL D 62 " pdb=" CA VAL D 62 " pdb=" C VAL D 62 " ideal model delta sigma weight residual 110.42 115.64 -5.22 9.60e-01 1.09e+00 2.96e+01 angle pdb=" CA ASP A 426 " pdb=" CB ASP A 426 " pdb=" CG ASP A 426 " ideal model delta sigma weight residual 112.60 118.00 -5.40 1.00e+00 1.00e+00 2.92e+01 angle pdb=" C GLN E 356 " pdb=" N ALA E 357 " pdb=" CA ALA E 357 " ideal model delta sigma weight residual 121.70 131.09 -9.39 1.80e+00 3.09e-01 2.72e+01 angle pdb=" CA ASP F 447 " pdb=" CB ASP F 447 " pdb=" CG ASP F 447 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 ... (remaining 24277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 10458 17.21 - 34.43: 561 34.43 - 51.64: 104 51.64 - 68.85: 35 68.85 - 86.06: 20 Dihedral angle restraints: 11178 sinusoidal: 4539 harmonic: 6639 Sorted by residual: dihedral pdb=" C ASN C 217 " pdb=" N ASN C 217 " pdb=" CA ASN C 217 " pdb=" CB ASN C 217 " ideal model delta harmonic sigma weight residual -122.60 -137.33 14.73 0 2.50e+00 1.60e-01 3.47e+01 dihedral pdb=" CA LYS B 143 " pdb=" C LYS B 143 " pdb=" N ILE B 144 " pdb=" CA ILE B 144 " ideal model delta harmonic sigma weight residual 180.00 151.27 28.73 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ILE D 201 " pdb=" C ILE D 201 " pdb=" N LYS D 202 " pdb=" CA LYS D 202 " ideal model delta harmonic sigma weight residual 180.00 -151.53 -28.47 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 11175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2160 0.111 - 0.222: 598 0.222 - 0.333: 72 0.333 - 0.444: 10 0.444 - 0.555: 2 Chirality restraints: 2842 Sorted by residual: chirality pdb=" CA ASN C 217 " pdb=" N ASN C 217 " pdb=" C ASN C 217 " pdb=" CB ASN C 217 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.70e+00 chirality pdb=" CA ASN C 146 " pdb=" N ASN C 146 " pdb=" C ASN C 146 " pdb=" CB ASN C 146 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" CA LYS C 416 " pdb=" N LYS C 416 " pdb=" C LYS C 416 " pdb=" CB LYS C 416 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 2839 not shown) Planarity restraints: 3089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 348 " -0.093 2.00e-02 2.50e+03 5.17e-02 5.34e+01 pdb=" CG TYR A 348 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 348 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR A 348 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR A 348 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR A 348 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR A 348 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 348 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 367 " -0.095 2.00e-02 2.50e+03 4.99e-02 4.98e+01 pdb=" CG TYR F 367 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 367 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR F 367 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR F 367 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR F 367 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR F 367 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR F 367 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 367 " -0.093 2.00e-02 2.50e+03 4.90e-02 4.80e+01 pdb=" CG TYR E 367 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR E 367 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR E 367 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR E 367 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR E 367 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR E 367 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 367 " -0.065 2.00e-02 2.50e+03 ... (remaining 3086 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 8109 3.01 - 3.48: 16679 3.48 - 3.95: 26243 3.95 - 4.43: 27660 4.43 - 4.90: 49233 Nonbonded interactions: 127924 Sorted by model distance: nonbonded pdb=" OE2 GLU F 303 " pdb=" OG1 THR F 322 " model vdw 2.533 3.040 nonbonded pdb=" OE2 GLU D 303 " pdb=" OG1 THR D 322 " model vdw 2.534 3.040 nonbonded pdb=" OE2 GLU B 303 " pdb=" OG1 THR B 322 " model vdw 2.538 3.040 nonbonded pdb=" OE2 GLU E 303 " pdb=" OG1 THR E 322 " model vdw 2.550 3.040 nonbonded pdb=" OE2 GLU A 303 " pdb=" OG1 THR A 322 " model vdw 2.552 3.040 ... (remaining 127919 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 45 through 101 or resid 105 through 271 or resid 274 throu \ gh 390 or resid 392 through 447)) selection = (chain 'B' and (resid 45 through 101 or resid 105 through 271 or resid 274 throu \ gh 390 or resid 414 through 447)) selection = (chain 'C' and (resid 45 through 271 or resid 274 through 390 or resid 392 throu \ gh 447)) selection = (chain 'D' and (resid 45 through 101 or resid 105 through 390 or resid 414 throu \ gh 447)) selection = (chain 'E' and (resid 45 through 101 or resid 105 through 271 or resid 274 throu \ gh 390 or resid 392 through 447)) selection = (chain 'F' and (resid 45 through 101 or resid 105 through 390 or resid 414 throu \ gh 447)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.290 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.012 0.045 18021 Z= 0.765 Angle : 1.826 9.392 24282 Z= 1.228 Chirality : 0.097 0.555 2842 Planarity : 0.013 0.210 3089 Dihedral : 12.493 86.065 6898 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.98 % Allowed : 3.34 % Favored : 95.68 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.16), residues: 2248 helix: -1.21 (0.16), residues: 729 sheet: 1.01 (0.28), residues: 327 loop : -1.05 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG B 49 TYR 0.095 0.019 TYR F 367 PHE 0.064 0.009 PHE D 105 TRP 0.035 0.009 TRP C 439 HIS 0.015 0.003 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.01238 (18021) covalent geometry : angle 1.82615 (24282) hydrogen bonds : bond 0.21912 ( 712) hydrogen bonds : angle 7.53264 ( 2037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7681 (m-40) cc_final: 0.7368 (m110) REVERT: A 376 ASN cc_start: 0.7059 (t0) cc_final: 0.6588 (t0) REVERT: B 330 MET cc_start: 0.8045 (ttt) cc_final: 0.7719 (ttp) REVERT: C 177 ASN cc_start: 0.7782 (m-40) cc_final: 0.7486 (m110) REVERT: C 337 ASP cc_start: 0.6639 (p0) cc_final: 0.5971 (t0) REVERT: E 71 MET cc_start: 0.9058 (mmp) cc_final: 0.8581 (mmp) REVERT: E 143 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8267 (mtpp) REVERT: E 376 ASN cc_start: 0.7837 (t0) cc_final: 0.7628 (t0) REVERT: F 92 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8125 (tppt) outliers start: 19 outliers final: 7 residues processed: 248 average time/residue: 0.1346 time to fit residues: 48.0218 Evaluate side-chains 149 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 196 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.0980 chunk 212 optimal weight: 1.9990 overall best weight: 1.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 266 GLN D 266 GLN F 100 GLN F 266 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.176088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117792 restraints weight = 22556.683| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.96 r_work: 0.3295 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18021 Z= 0.149 Angle : 0.614 6.433 24282 Z= 0.331 Chirality : 0.048 0.179 2842 Planarity : 0.005 0.052 3089 Dihedral : 5.579 57.330 2437 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.34 % Allowed : 5.19 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2248 helix: 0.87 (0.19), residues: 737 sheet: 0.78 (0.24), residues: 416 loop : -0.70 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.014 0.002 TYR F 347 PHE 0.011 0.001 PHE B 50 TRP 0.006 0.001 TRP A 439 HIS 0.004 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00337 (18021) covalent geometry : angle 0.61352 (24282) hydrogen bonds : bond 0.05053 ( 712) hydrogen bonds : angle 4.84796 ( 2037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7558 (m-40) cc_final: 0.7160 (m110) REVERT: B 92 LYS cc_start: 0.7765 (tmtt) cc_final: 0.7514 (ttpp) REVERT: B 330 MET cc_start: 0.7793 (ttt) cc_final: 0.7588 (ttm) REVERT: C 91 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7110 (mt-10) REVERT: C 337 ASP cc_start: 0.6736 (p0) cc_final: 0.6260 (p0) REVERT: E 143 LYS cc_start: 0.8291 (mtpp) cc_final: 0.7862 (mtpp) REVERT: E 190 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5906 (pp) REVERT: F 92 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7737 (tppt) REVERT: F 100 GLN cc_start: 0.8111 (tt0) cc_final: 0.7522 (tm-30) outliers start: 26 outliers final: 17 residues processed: 214 average time/residue: 0.1308 time to fit residues: 42.0273 Evaluate side-chains 163 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 446 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 155 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN C 170 GLN E 98 GLN F 266 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.172761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109735 restraints weight = 22439.405| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.29 r_work: 0.3130 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18021 Z= 0.146 Angle : 0.562 6.301 24282 Z= 0.301 Chirality : 0.048 0.173 2842 Planarity : 0.005 0.054 3089 Dihedral : 5.087 58.899 2435 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.70 % Allowed : 7.10 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2248 helix: 1.29 (0.19), residues: 736 sheet: 0.65 (0.25), residues: 408 loop : -0.78 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 188 TYR 0.016 0.002 TYR D 197 PHE 0.015 0.001 PHE F 105 TRP 0.005 0.001 TRP A 439 HIS 0.004 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00350 (18021) covalent geometry : angle 0.56211 (24282) hydrogen bonds : bond 0.05150 ( 712) hydrogen bonds : angle 4.50350 ( 2037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 156 ASP cc_start: 0.6541 (m-30) cc_final: 0.6126 (m-30) REVERT: A 177 ASN cc_start: 0.7557 (m-40) cc_final: 0.7163 (m110) REVERT: E 143 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7726 (mtpp) REVERT: F 100 GLN cc_start: 0.8063 (tt0) cc_final: 0.7464 (tm-30) outliers start: 33 outliers final: 26 residues processed: 178 average time/residue: 0.1241 time to fit residues: 33.6669 Evaluate side-chains 169 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 446 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 142 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.0030 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 162 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN E 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.177697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116313 restraints weight = 22533.968| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.26 r_work: 0.3238 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18021 Z= 0.094 Angle : 0.478 6.609 24282 Z= 0.254 Chirality : 0.045 0.158 2842 Planarity : 0.005 0.054 3089 Dihedral : 4.363 57.698 2431 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.23 % Allowed : 8.17 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.18), residues: 2248 helix: 1.70 (0.20), residues: 741 sheet: 0.45 (0.24), residues: 436 loop : -0.76 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.010 0.001 TYR F 347 PHE 0.007 0.001 PHE D 105 TRP 0.005 0.001 TRP A 439 HIS 0.002 0.000 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00203 (18021) covalent geometry : angle 0.47809 (24282) hydrogen bonds : bond 0.03321 ( 712) hydrogen bonds : angle 4.09577 ( 2037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7337 (m-40) cc_final: 0.6908 (m110) REVERT: D 303 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7748 (mt-10) REVERT: E 143 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7758 (mtpp) REVERT: E 190 ILE cc_start: 0.6075 (OUTLIER) cc_final: 0.5749 (pp) REVERT: F 100 GLN cc_start: 0.8001 (tt0) cc_final: 0.7428 (tm-30) REVERT: F 285 TYR cc_start: 0.8368 (m-80) cc_final: 0.8140 (m-80) outliers start: 24 outliers final: 17 residues processed: 179 average time/residue: 0.1239 time to fit residues: 33.9990 Evaluate side-chains 166 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 446 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 0 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 219 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 47 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN E 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.174935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113225 restraints weight = 22318.803| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.25 r_work: 0.3196 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18021 Z= 0.118 Angle : 0.503 5.694 24282 Z= 0.266 Chirality : 0.046 0.156 2842 Planarity : 0.005 0.053 3089 Dihedral : 4.371 55.031 2430 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.65 % Allowed : 7.92 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.18), residues: 2248 helix: 1.70 (0.20), residues: 741 sheet: 0.42 (0.25), residues: 429 loop : -0.75 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 162 TYR 0.014 0.001 TYR D 197 PHE 0.010 0.001 PHE D 323 TRP 0.004 0.001 TRP A 439 HIS 0.003 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00281 (18021) covalent geometry : angle 0.50338 (24282) hydrogen bonds : bond 0.04177 ( 712) hydrogen bonds : angle 4.13363 ( 2037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.6666 (m-30) cc_final: 0.6243 (m-30) REVERT: B 98 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7384 (mt0) REVERT: B 114 MET cc_start: 0.3603 (ttt) cc_final: 0.3266 (mtp) REVERT: D 114 MET cc_start: 0.2618 (mmt) cc_final: 0.1860 (mtt) REVERT: E 143 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7827 (mtpp) REVERT: E 190 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5826 (pp) REVERT: E 446 MET cc_start: 0.6959 (mmm) cc_final: 0.6484 (mtt) REVERT: F 100 GLN cc_start: 0.8019 (tt0) cc_final: 0.7419 (tm-30) outliers start: 32 outliers final: 26 residues processed: 177 average time/residue: 0.1262 time to fit residues: 33.8000 Evaluate side-chains 173 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 185 optimal weight: 0.6980 chunk 61 optimal weight: 0.0970 chunk 134 optimal weight: 0.2980 chunk 81 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 110 optimal weight: 0.2980 chunk 14 optimal weight: 10.0000 chunk 221 optimal weight: 0.0470 chunk 15 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.179326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118777 restraints weight = 22310.478| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.24 r_work: 0.3267 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18021 Z= 0.084 Angle : 0.447 5.524 24282 Z= 0.236 Chirality : 0.044 0.148 2842 Planarity : 0.004 0.051 3089 Dihedral : 3.886 53.312 2430 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.08 % Allowed : 9.05 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2248 helix: 1.99 (0.20), residues: 735 sheet: 0.35 (0.24), residues: 446 loop : -0.70 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.009 0.001 TYR F 347 PHE 0.009 0.001 PHE A 94 TRP 0.005 0.001 TRP A 439 HIS 0.001 0.000 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00179 (18021) covalent geometry : angle 0.44706 (24282) hydrogen bonds : bond 0.02698 ( 712) hydrogen bonds : angle 3.85357 ( 2037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7630 (mm-30) REVERT: B 98 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7460 (tt0) REVERT: B 114 MET cc_start: 0.3861 (ttt) cc_final: 0.3473 (mtp) REVERT: D 114 MET cc_start: 0.2741 (mmt) cc_final: 0.2105 (mtp) REVERT: E 125 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6463 (tt) REVERT: E 190 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5718 (pp) REVERT: F 100 GLN cc_start: 0.7973 (tt0) cc_final: 0.7427 (tm-30) REVERT: F 114 MET cc_start: 0.3311 (mtp) cc_final: 0.2942 (mtt) outliers start: 21 outliers final: 13 residues processed: 173 average time/residue: 0.1291 time to fit residues: 34.2133 Evaluate side-chains 158 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 446 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 127 optimal weight: 0.0870 chunk 124 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 50 optimal weight: 0.0570 chunk 168 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN C 146 ASN ** E 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.176087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114359 restraints weight = 22355.908| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.26 r_work: 0.3213 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18021 Z= 0.107 Angle : 0.489 9.052 24282 Z= 0.258 Chirality : 0.045 0.170 2842 Planarity : 0.004 0.056 3089 Dihedral : 4.016 51.278 2430 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.18 % Allowed : 8.95 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2248 helix: 1.88 (0.20), residues: 743 sheet: 0.45 (0.25), residues: 437 loop : -0.73 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 162 TYR 0.013 0.001 TYR F 347 PHE 0.009 0.001 PHE A 94 TRP 0.004 0.001 TRP F 439 HIS 0.002 0.000 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00249 (18021) covalent geometry : angle 0.48906 (24282) hydrogen bonds : bond 0.03773 ( 712) hydrogen bonds : angle 3.93395 ( 2037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.6616 (m-30) cc_final: 0.6249 (m-30) REVERT: B 69 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 98 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7432 (mt0) REVERT: B 114 MET cc_start: 0.3860 (ttt) cc_final: 0.3463 (mtp) REVERT: C 189 ASP cc_start: 0.8020 (t0) cc_final: 0.7582 (t0) REVERT: D 92 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7904 (tppt) REVERT: D 114 MET cc_start: 0.2681 (mmt) cc_final: 0.2060 (mtp) REVERT: E 125 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6528 (tt) REVERT: E 190 ILE cc_start: 0.6034 (OUTLIER) cc_final: 0.5692 (pp) REVERT: E 446 MET cc_start: 0.6936 (mmm) cc_final: 0.6468 (mtt) REVERT: F 46 MET cc_start: 0.7466 (mmm) cc_final: 0.6881 (mmm) REVERT: F 100 GLN cc_start: 0.8013 (tt0) cc_final: 0.7497 (tm-30) REVERT: F 114 MET cc_start: 0.3307 (mtp) cc_final: 0.2947 (mtt) outliers start: 23 outliers final: 19 residues processed: 172 average time/residue: 0.1259 time to fit residues: 33.2933 Evaluate side-chains 169 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 292 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 37 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 194 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN C 146 ASN ** E 45 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 = 0.4018 r_free = 0.4018 target = 0.172005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109448 restraints weight = 22226.801| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.22 r_work: 0.3154 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18021 Z= 0.174 Angle : 0.565 8.829 24282 Z= 0.297 Chirality : 0.048 0.185 2842 Planarity : 0.005 0.056 3089 Dihedral : 4.533 48.868 2430 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.70 % Allowed : 8.64 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2248 helix: 1.56 (0.20), residues: 740 sheet: 0.25 (0.25), residues: 439 loop : -0.87 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 162 TYR 0.021 0.002 TYR D 197 PHE 0.015 0.001 PHE F 323 TRP 0.004 0.001 TRP F 439 HIS 0.004 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00437 (18021) covalent geometry : angle 0.56457 (24282) hydrogen bonds : bond 0.05371 ( 712) hydrogen bonds : angle 4.28829 ( 2037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 156 ASP cc_start: 0.6659 (m-30) cc_final: 0.6273 (m-30) REVERT: B 98 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7406 (mt0) REVERT: B 336 LYS cc_start: 0.8595 (tptt) cc_final: 0.8190 (pptt) REVERT: C 189 ASP cc_start: 0.8046 (t0) cc_final: 0.7632 (t0) REVERT: E 125 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6702 (tt) REVERT: E 143 LYS cc_start: 0.8269 (mtpp) cc_final: 0.8005 (mtpp) REVERT: E 190 ILE cc_start: 0.6209 (OUTLIER) cc_final: 0.5874 (pp) REVERT: E 446 MET cc_start: 0.7159 (mmm) cc_final: 0.6719 (mtt) REVERT: F 100 GLN cc_start: 0.8075 (tt0) cc_final: 0.7527 (tm-30) REVERT: F 114 MET cc_start: 0.3232 (mtp) cc_final: 0.2885 (mtt) outliers start: 33 outliers final: 24 residues processed: 173 average time/residue: 0.1255 time to fit residues: 32.9858 Evaluate side-chains 169 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 155 optimal weight: 0.0270 chunk 34 optimal weight: 8.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN C 146 ASN ** E 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN F 266 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.174919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113279 restraints weight = 22278.815| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.23 r_work: 0.3198 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18021 Z= 0.108 Angle : 0.487 8.226 24282 Z= 0.258 Chirality : 0.045 0.153 2842 Planarity : 0.004 0.054 3089 Dihedral : 4.185 46.355 2430 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.34 % Allowed : 9.10 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2248 helix: 1.75 (0.20), residues: 743 sheet: 0.20 (0.25), residues: 438 loop : -0.87 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 162 TYR 0.013 0.001 TYR D 197 PHE 0.011 0.001 PHE A 94 TRP 0.005 0.001 TRP F 439 HIS 0.002 0.000 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00254 (18021) covalent geometry : angle 0.48706 (24282) hydrogen bonds : bond 0.03800 ( 712) hydrogen bonds : angle 4.03037 ( 2037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 156 ASP cc_start: 0.6603 (m-30) cc_final: 0.6235 (m-30) REVERT: B 98 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7510 (mt0) REVERT: C 189 ASP cc_start: 0.7995 (t0) cc_final: 0.7588 (t0) REVERT: E 125 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6687 (tt) REVERT: E 190 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5678 (pp) REVERT: E 446 MET cc_start: 0.6935 (mmm) cc_final: 0.6516 (mtt) REVERT: F 100 GLN cc_start: 0.7968 (tt0) cc_final: 0.7478 (tm-30) REVERT: F 114 MET cc_start: 0.3128 (mtp) cc_final: 0.2787 (mtt) outliers start: 26 outliers final: 23 residues processed: 171 average time/residue: 0.1390 time to fit residues: 36.2265 Evaluate side-chains 171 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 101 optimal weight: 0.0020 chunk 24 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 209 optimal weight: 0.0470 chunk 207 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.7490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN C 146 ASN ** E 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN F 266 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.176090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114719 restraints weight = 22098.865| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.22 r_work: 0.3211 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18021 Z= 0.098 Angle : 0.480 8.456 24282 Z= 0.252 Chirality : 0.044 0.149 2842 Planarity : 0.004 0.053 3089 Dihedral : 3.917 33.963 2428 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.13 % Allowed : 9.20 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2248 helix: 1.85 (0.20), residues: 743 sheet: 0.24 (0.25), residues: 438 loop : -0.82 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 162 TYR 0.012 0.001 TYR D 197 PHE 0.011 0.001 PHE A 94 TRP 0.005 0.001 TRP F 439 HIS 0.002 0.000 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00225 (18021) covalent geometry : angle 0.47974 (24282) hydrogen bonds : bond 0.03509 ( 712) hydrogen bonds : angle 3.92998 ( 2037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 156 ASP cc_start: 0.6585 (m-30) cc_final: 0.6213 (m-30) REVERT: B 98 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7571 (tt0) REVERT: C 189 ASP cc_start: 0.7898 (t0) cc_final: 0.7485 (t0) REVERT: E 125 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6671 (tt) REVERT: E 190 ILE cc_start: 0.6025 (OUTLIER) cc_final: 0.5702 (pp) REVERT: E 446 MET cc_start: 0.6883 (mmm) cc_final: 0.6450 (mtt) REVERT: F 100 GLN cc_start: 0.7960 (tt0) cc_final: 0.7486 (tm-30) REVERT: F 114 MET cc_start: 0.3120 (mtp) cc_final: 0.2869 (mtt) outliers start: 22 outliers final: 18 residues processed: 165 average time/residue: 0.1215 time to fit residues: 31.1894 Evaluate side-chains 164 residues out of total 1945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 266 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 56 optimal weight: 0.3980 chunk 86 optimal weight: 0.0670 chunk 213 optimal weight: 4.9990 chunk 146 optimal weight: 0.0670 chunk 183 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 6 optimal weight: 0.0010 chunk 101 optimal weight: 4.9990 chunk 143 optimal weight: 0.1980 chunk 46 optimal weight: 0.0270 overall best weight: 0.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN C 146 ASN F 266 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.181454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121579 restraints weight = 22373.493| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.23 r_work: 0.3315 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18021 Z= 0.083 Angle : 0.447 7.974 24282 Z= 0.235 Chirality : 0.043 0.147 2842 Planarity : 0.004 0.049 3089 Dihedral : 3.400 20.510 2428 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.77 % Allowed : 9.61 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 2248 helix: 2.14 (0.20), residues: 724 sheet: 0.14 (0.24), residues: 456 loop : -0.71 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.009 0.001 TYR F 277 PHE 0.011 0.000 PHE A 94 TRP 0.006 0.001 TRP A 439 HIS 0.001 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00179 (18021) covalent geometry : angle 0.44656 (24282) hydrogen bonds : bond 0.02260 ( 712) hydrogen bonds : angle 3.67708 ( 2037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3811.60 seconds wall clock time: 65 minutes 55.92 seconds (3955.92 seconds total)