Starting phenix.real_space_refine on Tue Jun 10 23:41:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k21_22639/06_2025/7k21_22639.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k21_22639/06_2025/7k21_22639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k21_22639/06_2025/7k21_22639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k21_22639/06_2025/7k21_22639.map" model { file = "/net/cci-nas-00/data/ceres_data/7k21_22639/06_2025/7k21_22639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k21_22639/06_2025/7k21_22639.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7480 2.51 5 N 1984 2.21 5 O 2284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11848 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.68, per 1000 atoms: 0.65 Number of scatterers: 11848 At special positions: 0 Unit cell: (100.32, 76.285, 164.065, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 12 15.00 Mg 4 11.99 O 2284 8.00 N 1984 7.00 C 7480 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.6 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 24 sheets defined 43.8% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.530A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.843A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.522A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.793A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.684A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.552A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.151A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.543A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 267' Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.906A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 359 through 366 removed outlier: 4.230A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.547A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.542A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.849A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.791A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.693A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 252 through 257 removed outlier: 4.095A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.569A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.946A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 359 through 366 removed outlier: 4.160A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 removed outlier: 3.592A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.540A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.864A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.849A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.631A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 252 through 257 removed outlier: 4.119A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.615A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.975A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 359 through 366 removed outlier: 4.248A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 370 removed outlier: 3.540A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 370' Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.514A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.865A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.553A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.652A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 252 through 257 removed outlier: 4.121A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.597A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.890A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 Processing helix chain 'D' and resid 337 through 348 removed outlier: 3.531A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 4.117A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 370 removed outlier: 3.526A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 370' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.838A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.733A pdb=" N LYS A 68 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.532A pdb=" N SER A 155 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.875A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.565A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.567A pdb=" N SER B 155 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.845A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.626A pdb=" N LYS C 68 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.567A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.824A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.538A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.637A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 467 hydrogen bonds defined for protein. 1206 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: 3.70 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3637 1.33 - 1.45: 1782 1.45 - 1.57: 6533 1.57 - 1.69: 12 1.69 - 1.80: 148 Bond restraints: 12112 Sorted by residual: bond pdb=" O4 PO4 A 803 " pdb=" P PO4 A 803 " ideal model delta sigma weight residual 1.568 1.500 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O4 PO4 B 803 " pdb=" P PO4 B 803 " ideal model delta sigma weight residual 1.568 1.500 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O4 PO4 D 803 " pdb=" P PO4 D 803 " ideal model delta sigma weight residual 1.568 1.501 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O4 PO4 C 803 " pdb=" P PO4 C 803 " ideal model delta sigma weight residual 1.568 1.501 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O3 PO4 B 803 " pdb=" P PO4 B 803 " ideal model delta sigma weight residual 1.569 1.502 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 12107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 15953 2.15 - 4.31: 409 4.31 - 6.46: 66 6.46 - 8.61: 20 8.61 - 10.77: 4 Bond angle restraints: 16452 Sorted by residual: angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 116.68 -6.18 1.70e+00 3.46e-01 1.32e+01 angle pdb=" C19 1T4 B 804 " pdb=" C17 1T4 B 804 " pdb=" N1 1T4 B 804 " ideal model delta sigma weight residual 114.67 125.44 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" N HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.50 116.51 -6.01 1.70e+00 3.46e-01 1.25e+01 angle pdb=" C19 1T4 D 804 " pdb=" C17 1T4 D 804 " pdb=" N1 1T4 D 804 " ideal model delta sigma weight residual 114.67 125.18 -10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C19 1T4 C 804 " pdb=" C17 1T4 C 804 " pdb=" N1 1T4 C 804 " ideal model delta sigma weight residual 114.67 125.01 -10.34 3.00e+00 1.11e-01 1.19e+01 ... (remaining 16447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.95: 6992 20.95 - 41.89: 205 41.89 - 62.84: 9 62.84 - 83.78: 10 83.78 - 104.73: 4 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" O1B ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " pdb=" PA ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 -164.73 104.73 1 2.00e+01 2.50e-03 3.01e+01 dihedral pdb=" O1B ADP D 802 " pdb=" O3A ADP D 802 " pdb=" PB ADP D 802 " pdb=" PA ADP D 802 " ideal model delta sinusoidal sigma weight residual -60.00 -159.76 99.76 1 2.00e+01 2.50e-03 2.81e+01 dihedral pdb=" O1B ADP C 802 " pdb=" O3A ADP C 802 " pdb=" PB ADP C 802 " pdb=" PA ADP C 802 " ideal model delta sinusoidal sigma weight residual -60.00 -157.82 97.82 1 2.00e+01 2.50e-03 2.73e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1288 0.057 - 0.115: 451 0.115 - 0.172: 56 0.172 - 0.229: 5 0.229 - 0.287: 8 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1805 not shown) Planarity restraints: 2092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO A 164 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " -0.019 2.00e-02 2.50e+03 1.34e-02 4.48e+00 pdb=" CG TRP D 340 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 340 " -0.019 2.00e-02 2.50e+03 1.31e-02 4.29e+00 pdb=" CG TRP A 340 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 340 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 340 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 340 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 340 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 340 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 340 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 340 " -0.003 2.00e-02 2.50e+03 ... (remaining 2089 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 160 2.63 - 3.20: 9964 3.20 - 3.77: 18163 3.77 - 4.33: 27392 4.33 - 4.90: 43761 Nonbonded interactions: 99440 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.066 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.070 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 2.075 2.170 nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR A 202 " pdb=" OE1 GLU A 205 " model vdw 2.223 3.040 ... (remaining 99435 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.380 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.008 0.231 12116 Z= 0.499 Angle : 0.866 10.768 16452 Z= 0.436 Chirality : 0.057 0.287 1808 Planarity : 0.007 0.053 2092 Dihedral : 10.390 104.727 4468 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.17), residues: 1468 helix: -4.24 (0.09), residues: 592 sheet: -1.26 (0.41), residues: 136 loop : -1.73 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP D 340 HIS 0.011 0.003 HIS C 88 PHE 0.021 0.003 PHE A 124 TYR 0.030 0.003 TYR C 69 ARG 0.015 0.001 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.28042 ( 457) hydrogen bonds : angle 9.87074 ( 1206) covalent geometry : bond 0.00743 (12112) covalent geometry : angle 0.86564 (16452) Misc. bond : bond 0.21086 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 299 MET cc_start: 0.8549 (mtm) cc_final: 0.8223 (mtm) outliers start: 0 outliers final: 1 residues processed: 125 average time/residue: 1.4331 time to fit residues: 193.1249 Evaluate side-chains 89 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 88 HIS A 161 HIS B 40 HIS B 88 HIS B 161 HIS C 88 HIS C 161 HIS C 296 ASN D 88 HIS D 161 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.078734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.065162 restraints weight = 23254.022| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.32 r_work: 0.2783 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12116 Z= 0.155 Angle : 0.613 6.758 16452 Z= 0.305 Chirality : 0.046 0.148 1808 Planarity : 0.005 0.048 2092 Dihedral : 8.726 88.564 1674 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.72 % Allowed : 6.29 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.20), residues: 1468 helix: -2.18 (0.17), residues: 568 sheet: -0.90 (0.32), residues: 228 loop : -0.53 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 340 HIS 0.004 0.001 HIS D 88 PHE 0.010 0.002 PHE B 90 TYR 0.008 0.001 TYR A 69 ARG 0.007 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 457) hydrogen bonds : angle 5.45396 ( 1206) covalent geometry : bond 0.00351 (12112) covalent geometry : angle 0.61251 (16452) Misc. bond : bond 0.00062 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.276 Fit side-chains REVERT: A 12 ASN cc_start: 0.8655 (p0) cc_final: 0.8446 (p0) REVERT: B 299 MET cc_start: 0.9161 (mtm) cc_final: 0.8893 (mtm) REVERT: D 184 ASP cc_start: 0.9005 (m-30) cc_final: 0.8805 (m-30) REVERT: D 205 GLU cc_start: 0.8846 (mp0) cc_final: 0.8537 (mt-10) outliers start: 9 outliers final: 0 residues processed: 100 average time/residue: 1.4234 time to fit residues: 155.1458 Evaluate side-chains 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.077685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.063782 restraints weight = 23660.532| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.39 r_work: 0.2757 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12116 Z= 0.175 Angle : 0.586 6.442 16452 Z= 0.286 Chirality : 0.047 0.155 1808 Planarity : 0.004 0.045 2092 Dihedral : 7.995 83.219 1672 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.64 % Allowed : 7.72 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.22), residues: 1468 helix: -0.70 (0.21), residues: 556 sheet: -1.03 (0.30), residues: 268 loop : 0.07 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.004 0.001 HIS C 88 PHE 0.010 0.001 PHE D 262 TYR 0.013 0.001 TYR D 69 ARG 0.008 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 457) hydrogen bonds : angle 4.81300 ( 1206) covalent geometry : bond 0.00410 (12112) covalent geometry : angle 0.58623 (16452) Misc. bond : bond 0.00026 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 1.344 Fit side-chains REVERT: A 12 ASN cc_start: 0.8761 (p0) cc_final: 0.8536 (p0) REVERT: B 205 GLU cc_start: 0.8811 (mp0) cc_final: 0.8517 (mp0) REVERT: B 299 MET cc_start: 0.9233 (mtm) cc_final: 0.9003 (mtm) REVERT: D 184 ASP cc_start: 0.8993 (m-30) cc_final: 0.8771 (m-30) REVERT: D 205 GLU cc_start: 0.8841 (mp0) cc_final: 0.8505 (mt-10) outliers start: 8 outliers final: 0 residues processed: 96 average time/residue: 1.3089 time to fit residues: 137.2724 Evaluate side-chains 86 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.078248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.064573 restraints weight = 23299.131| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.34 r_work: 0.2771 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12116 Z= 0.136 Angle : 0.553 6.414 16452 Z= 0.265 Chirality : 0.045 0.141 1808 Planarity : 0.004 0.043 2092 Dihedral : 7.731 85.529 1672 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.11 % Allowed : 7.96 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1468 helix: -0.08 (0.23), residues: 556 sheet: -0.79 (0.31), residues: 268 loop : 0.36 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.004 0.001 HIS D 161 PHE 0.007 0.001 PHE C 31 TYR 0.010 0.001 TYR D 69 ARG 0.004 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 457) hydrogen bonds : angle 4.57063 ( 1206) covalent geometry : bond 0.00319 (12112) covalent geometry : angle 0.55342 (16452) Misc. bond : bond 0.00016 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.367 Fit side-chains REVERT: B 44 MET cc_start: 0.8867 (mtt) cc_final: 0.8615 (mtt) REVERT: B 205 GLU cc_start: 0.8802 (mp0) cc_final: 0.8543 (mp0) REVERT: D 184 ASP cc_start: 0.8967 (m-30) cc_final: 0.8749 (m-30) REVERT: D 205 GLU cc_start: 0.8844 (mp0) cc_final: 0.8424 (mt-10) outliers start: 14 outliers final: 2 residues processed: 96 average time/residue: 1.2667 time to fit residues: 132.6896 Evaluate side-chains 88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 355 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 12 ASN C 59 GLN D 12 ASN D 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.076782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.062976 restraints weight = 23524.431| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.35 r_work: 0.2733 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12116 Z= 0.206 Angle : 0.589 6.500 16452 Z= 0.284 Chirality : 0.047 0.159 1808 Planarity : 0.004 0.043 2092 Dihedral : 7.757 84.086 1672 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.27 % Allowed : 8.36 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.23), residues: 1468 helix: 0.09 (0.23), residues: 560 sheet: -0.66 (0.31), residues: 268 loop : 0.46 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.005 0.001 HIS D 161 PHE 0.010 0.001 PHE D 262 TYR 0.010 0.001 TYR A 306 ARG 0.004 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 457) hydrogen bonds : angle 4.46298 ( 1206) covalent geometry : bond 0.00489 (12112) covalent geometry : angle 0.58887 (16452) Misc. bond : bond 0.00019 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.583 Fit side-chains REVERT: B 44 MET cc_start: 0.8930 (mtt) cc_final: 0.8676 (mtt) REVERT: B 205 GLU cc_start: 0.8836 (mp0) cc_final: 0.8322 (mt-10) REVERT: D 184 ASP cc_start: 0.8983 (m-30) cc_final: 0.8777 (m-30) REVERT: D 205 GLU cc_start: 0.8859 (mp0) cc_final: 0.8416 (mt-10) REVERT: D 288 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7767 (p0) outliers start: 16 outliers final: 2 residues processed: 96 average time/residue: 1.2995 time to fit residues: 136.1490 Evaluate side-chains 95 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 288 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.3409 > 50: distance: 53 - 73: 5.846 distance: 62 - 90: 8.240 distance: 65 - 73: 7.797 distance: 66 - 99: 10.861 distance: 73 - 74: 7.495 distance: 74 - 75: 7.791 distance: 74 - 77: 6.731 distance: 75 - 76: 11.676 distance: 75 - 81: 5.320 distance: 76 - 108: 9.714 distance: 77 - 78: 18.806 distance: 78 - 79: 24.124 distance: 79 - 80: 13.377 distance: 81 - 82: 5.421 distance: 82 - 83: 8.568 distance: 82 - 85: 4.101 distance: 83 - 84: 16.427 distance: 83 - 90: 6.032 distance: 84 - 116: 13.466 distance: 85 - 86: 7.334 distance: 86 - 87: 6.149 distance: 87 - 88: 3.066 distance: 90 - 91: 3.998 distance: 91 - 92: 3.868 distance: 91 - 94: 8.001 distance: 92 - 93: 6.096 distance: 92 - 99: 7.926 distance: 94 - 95: 10.708 distance: 95 - 96: 12.503 distance: 96 - 97: 5.751 distance: 97 - 98: 10.494 distance: 99 - 100: 6.100 distance: 100 - 101: 7.927 distance: 100 - 103: 6.942 distance: 101 - 102: 17.525 distance: 101 - 108: 8.350 distance: 103 - 104: 12.430 distance: 104 - 105: 10.177 distance: 105 - 106: 16.071 distance: 105 - 107: 7.611 distance: 108 - 109: 6.781 distance: 109 - 110: 4.845 distance: 109 - 112: 7.721 distance: 110 - 111: 17.522 distance: 110 - 116: 3.967 distance: 112 - 113: 3.537 distance: 112 - 114: 13.372 distance: 113 - 115: 4.516 distance: 116 - 117: 7.695 distance: 117 - 118: 12.482 distance: 117 - 120: 6.210 distance: 118 - 119: 14.449 distance: 118 - 123: 11.737 distance: 120 - 121: 8.754 distance: 120 - 122: 29.178 distance: 123 - 124: 9.155 distance: 124 - 125: 18.805 distance: 124 - 127: 18.805 distance: 125 - 126: 23.652 distance: 125 - 128: 19.664 distance: 128 - 129: 23.213 distance: 129 - 130: 22.176 distance: 129 - 132: 25.364 distance: 130 - 131: 6.427 distance: 130 - 136: 14.881 distance: 132 - 133: 27.042 distance: 133 - 134: 28.575 distance: 133 - 135: 22.400 distance: 136 - 137: 7.733 distance: 137 - 138: 13.687 distance: 137 - 140: 10.927 distance: 138 - 139: 5.699 distance: 138 - 141: 10.294 distance: 141 - 147: 4.752 distance: 142 - 143: 9.962 distance: 142 - 145: 6.057 distance: 143 - 144: 8.726 distance: 143 - 148: 10.536 distance: 145 - 146: 12.972 distance: 146 - 147: 18.164